The General Case
So, most answers here already cover the general ideas, but I will go over them as well.
The idea of the adventuring day as stated is to try and fairly balance the different classes, some which depend on short rests, some which depend on long rests. As noted in this question, changing the adventuring day to a shorter version, which is what you are planning to do, changes the balance of the game in favor of classes with bursty, recover-on-long-rest resources. A Wizard now may use all of its spells against the enemies in the first two encounters, because these are all the encounters.
If you try to balance that, for example, by making the encounters significantly stronger, that will make the encounter problematic for classes that don't have that many resources to begin with, because they are supposed to recover them at their short rest.
This creates a huge imbalance within the classes, making some classes greatly stronger than others, which is usually perceived as a problem.
I do not know any way of solving this issue in a general setting. If you remove short rests, you are making classes that depend on short rests weaker, just like if you put a giant anti-magic field in the campaign you make classes that depend on magic weaker.
However, in your case, the lack of short rests is not due to an actually shorter adventuring day, rather due to the (lack of) plausibility of taking a rest after the enemies have been warned.
In that case, instead of depleting the resources through combat (i.e., enemies that actually see the PCs and would call for other enemies), you can slowly take away their resources while not making them perceived by the enemy forces yet, thus, allowing for a short rest.
So, this is the first general advice:
Deplete their resources and Do allow Short Rests
In this sense, SeriousBri's answer is probably better than what I can advice you, but note that it is generally hard to take away resources such as Action Surges, Spell Slots and others with traps and other non-combat stuff. The only way I found that worked in my groups was through puzzles that required some specific resource to be spent. I have used a "Damage check door" which required the characters to deal some target amount of damage in a single round in order to open it (forcing them to spend resources as it was virtually impossible to deal that amount of damage without spending some stuff), runes that would only activate if someone cast a Fireball on them, and other ways to consume resources (that I obviously knew they had because I designed them after knowing what the party was :P).
In your case, it is quite hard to do thematically, since they are invading an enemy fortress, and having that fortress to have something "tailored" for the characters to overcome sounds awkward. But maybe one of the main enemies is a beast shapeshifter, and he has a locked vault that can only be opened by... a Bear! - essentially forcing your Druid to spend one of his transformations on it. This idea is a little far fetched and the example is quite silly, I admit, but I hope it is good enough for you to see the idea - and I am sure you are able to think on something along these lines that makes sense in your setting and that your players will appreciate (personally I would love to be the Druid and have a challenge that has to be overcome by me transforming in some animal).
Very important note: If you follow this idea, make sure you give enough clues for your characters so they understand what must be done and not waste more resources than you expected. In the Fireball example, it would be quite bad if they first tried Burning Hands, Scorching Ray and Chromatic Orb - Fire before actually trying a Fireball - that would lead to way more resources spent than I planned and would make the following encounters nearly impossible.
Your specific party case
The thing is: Your party consists of two rogues and a moon druid. Rogues are, in fact, remarkable for being almost a resourceless class. The only resource they care about is HP, essentially. They do not get spell slots (not the Thief or the Assassin at least), extra consumable dice, or any kind of feature recovered on-reset. That makes it considerably easier for you to balance out.
The Druid, as well, only has one relevant short rest resource: their beast transformations. With a one-hour-long transformation, that should not be a problem in terms of resource, either, and most likely they are going to be transformed for most of the combats at this level in any adventure.
So, from my point of view, the only resource you should worry about is their HP. This is the easiest resource to take a little bit away.
Make it a little bit harder
Unless your enemies already deal high damage, you can slightly increase the damage of the enemies - not enough to make it a whole CR higher, but enough to be noticeable in that they may leave the two-encounters-in-a-row in a very bad shape, maybe even dropping one of the Rogues' HP to zero (make no mistake: he should not die).
Alternatively, you can set traps - traps that deal damage are, well, the easiest and most common ones, compared to traps that force a spell slot to be spent - so they arrive at the encounters missing a few HP.
As a final alternative, I have found out that giving surprise to the enemies is a huge advantage for them and will make the combats considerably harder, without effectively increasing any damage dice, modifier or HP of the monsters/NPCs. Instead of rushing towards your party when they notice the invasion, they may handle it a little bit better and wait for a moment where they will have the upper hand. The guards will not immediately ask for help, though, as they want the glory of defeating the invaders for themselves, and will only ask for help when they notice the invaders are stronger than they initially thought. (Surely surprising your party is not that easy, but it is a possibility for balancing it).
Give them ways of recovering resources and make them go through a "normal" adventuring day
What is more interesting about the particular party setup you have is that you can give them ways of recovering their most important resource - HP - that are not short rests. Give the Druid a Cure Wounds scroll. Give them a few Potions of Healing. Then you can actually make them go through a few more encounters, and almost look like a "normal" adventuring day, but without short rests between the encounters. Give them enough potions and 1 minute to actually drink them and your party can even go through 4-6 encounters in a row, which is something most parties would have a problem even if they had a significant number of potions, because they have other important resources, like Ki Points or Action Surges or Warlock Spell Slots.
Ultimately, if, due to the nature of your party (two rogues and a druid), they can effectively invade in a very stealthy way and go through only one encounter, for example, these extra resources (potions and scrolls) you gave them become a reward for handling the challenge in a more efficient way, otherwise, they just spent what they were supposed to spend and no harms done.