This will probably work
The Zone of Truth spell's text is fairly unambiguous on the knowledge gained by the caster (PHB p. 289, bold added):
Until the spell ends, a creature that enters the spell’s area for the first time on a turn or starts its turn there must make a Charisma saving throw. [...] You know whether each creature succeeds or fails on its saving throw.
Now as a DM you could declare that this knowledge is contingent on awareness of a creature's existence, but that would be adding restrictions not present in the current spell. As written, it seems like any time any creature in the radius succeeds at or fails against this save, the caster knows.
Why this is balanced
Honestly, a 2nd level spell should reveal the presence of invisible creatures. After all, they already do. The spell See Invisibility (2nd level) not only reveals that an invisible creature is present but also lets you see it. And the 1st level spell Alarm will let you detect when any (invisible) creature enters a restricted space for 8 hours, not just 10 minutes (and is a ritual so could be cast without any resource expenditure but time).
Keep in mind that invisible creatures aren't always undetectable by default. An unseen creature is usually making enough noise that everyone knows where it is unless it attempts to Hide. So your party's passive perception may also be enough to reveal the presence of invisible creatures (though they will still be invisible).
All this is to say that your players realizing that Zone of Truth could reveal hidden creatures is not as unbalancing as it might initially seem. That being said, you had further specific questions about how to respond to this tactic:
What could you do about it?
There's plenty of options, but a few jump out:
Have the spell reveal invisible but benign creatures.
As I read it, this spell will let characters know about invisible enemies, but also other creatures. You could tell your players that something has failed at a saving throw, but no other information. If they all proceed to attack it, they may determine that they've spent a round in combat slaughtering a Sprite passing through the dungeon about its own business.
Have enemies go around the Zone of Truth
The description of Zone of Truth is unclear on whether or not the zone itself is visible. If you declare it to be visible, then creatures attempting to avoid detection could simply move around it (if possible). Even if you decided the spherical zone of truth was invisible, creatures could quickly determine where it is because...
The spell reveals the casters as much as it reveals the targets
Note that according to the text of Zone of Truth (ibid).
An affected creature is aware of the spell and can thus avoid answering questions to which it would normally respond with a lie.
As such, whenever an enemy steps into the Zone of Truth, they will realize that someone has cast that spell there (if they fail the saving throw). It's possible they weren't aware that the PCs were in the area before, but now they certainly are. So the spell essentially gives as much as it takes in this respect.
Have enemies rush through the zone
Note that Zone of Truth won't reveal where invisible enemies are exactly: just that they are somewhere in the area of effect of the spell when they fail or succeed at the saving throw (credit to Medix2 for pointing this out). Enemies could enter the zone of truth, then simply walk out of it. The PCs would know how many invisible enemies are present, but not know where they are. In many situations, this would give the invisible enemies most of the same advantages they had before (minus the possibility of surprising their foes).
On a personal note, I want to add that none of those tactics are my preferred ones. I'd suggest this final one as an alternative.
Let this tactic work.
This is a creative and clever use of this spell that thinks outside the box. Such an insight should be rewarded. If your players want to dedicate resources to safeguarding themselves from invisible enemies, this is a viable way to do so (and provides the benefit only of a lower level spell, Alarm, and for less time).
If you want this tactic to fail, I'd suggest there should be some compelling reason that it does (such as the enemy they are fighting is intimately familiar with the way they operate).