No, your necromancer's hit point maximum is not reduced.
Conversely, you can raise your homonculus' hit point maximum without your necromancer reducing his hit point maximum.
Inured to Undeath states
your hit point maximum can't be reduced
This is a very straightforward effect. Since specific beats general and this rules specifically says that it's not possible for your hit point maximum to be reduced, it simply cannot happen unless an even more specific rule says so.
Does Create Homunculus override Inured to Undeath?
We intuitively accept that Inured to Undeath allows you to ignore hit point maximum reductions from the attack of undead creatures such as a Specter. Let's look at how the Specter applies the hit point maximum reduction:
its hit point maximum is reduced by an amount equal to the damage taken
Now lets look at how Create Homunculus applies the hit point maximum reduction:
Your hit point maximum is reduced by the total
Both of these sentences effectively read as:
[a creature's] hit point maximum is reduced by [a number]
Since they say the same thing and don't use any wording that makes us think they should override your specific ability of ignoring hit point maximum reductions, Inured to Undeath applies here.
Create Homunculus does go on to state the following:
The reduction to your hit point maximum can’t be removed by any means before then, except by the homunculus‘s death.
That is a specific rule but it only stops you from removing the hit point maximum reduction. Since your hit points were never reduced, that is not an issue for you.
Will my Homonculus' hit point maximum increase anyway?
Now that we know that you can ignore the hit point maximum reduction, does your homonculus still get to increase his hit point maximum?
Here are the rules that determine how large the hit point maximum exchange is supposed to be:
Whenever you finish a long rest, you can spend up to half your Hit Dice if the homunculus is on the same plane of existence as you. When you do so, roll each die and add your Constitution modifier to it.
The bold text shows you how to calculate the total by which each creature's hit point maximum will change.
Let's look at the next sentence which performs the hit point maximum transfer:
Your hit point maximum is reduced by the total, and the homunculus’s hit point maximum and current hit points are both increased by it.
Here we are applying 2 separate effects:
- The first effect is to reduce your hit point maximum by the total.
- The second effect is to reduce your hit point maximum by it which clearly refers to the total.
Note that the second effect only refers to the total which was calculated when you rolled the dice and not to the amount by which your hit point maximum was actually reduced. This means that getting around the hit point maximum reduction doesn't stop your homunculus from raising his hit point maximum at all.
This interpretation is supported by the Sage Advice Compendium as of at least version 2.5.