It will probably work
The text of the spell is quite clear on the knowledge acquired by the caster (PHB p. 289, bold added):
Until the end of the spell, a creature
Who enters the spell area for the first time during a turn or begins his turn there must make a Charisma saving throw … You know if each creature succeeds or fails on its save throw.
Now, as a DM, you can declare that this knowledge depends on awareness of the existence of a creature, but that would add restrictions not present in the current spell. As written, it seems that whenever a creature in the ray succeeds or fails against this save, the launcher 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) reveals not only that an invisible creature is present but also lets you see it. And the 1st level spell Alarm will allow you to detect when an (invisible) creature enters a tight space for 8 hours, not just 10 minutes (and it is a ritual that could be started without any resource expenditure but time).
Keep in mind that invisible creatures aren't always undetectable by default. An invisible creature usually makes enough noise for everyone to know where it is unless it tries to hide. Thus, the passive perception of your group can also be sufficient to reveal the presence of invisible creatures (although they are always invisible).
All this to say that the fact that your players realize that Zone of Truth could reveal hidden creatures isn't as unbalanced as it initially appears. That being said, you had other specific questions on how to respond to this tactic:
What could you do there?
There are a lot of options, but a few are skipping.
- Ask the spell to reveal invisible but benign creatures.
As I read it, this spell will allow the characters to know the invisible enemies, but also other creatures. You could tell your players that something failed on a save throw, but no other information. If they all start attacking it, they can determine that they have spent a round in combat shooting down a Sprite passing through the dungeon about their own business.
- Ask enemies to bypass the Zone of Truth
It is not clear from the description of Zone of Truth whether the zone itself is visible. If you declare it visible, creatures that try to avoid detection can simply move (if possible). Even if you have decided that the spherical area of truth is invisible, creatures could quickly determine where it is because …
- The spell reveals the launchers as much as it reveals the targets
Note that according to the text of Area of truth (Ibid).
Affected creature is aware of the spell and can thus avoid answering questions which he would normally answer with a lie.
So every time an enemy enters the Truth Zone, they will realize that someone has cast the spell there (if they fail on the saving throw). They may not have known the PCs were in the area before, but now they certainly are. So the spell essentially gives as much as it takes in this regard.
- Ask enemies to rush into the area
Note that Area of truth will not reveal or the invisible enemies are exactly: just that they are somewhere in the area of effect of the spell when they fail or succeed the saving throw (credit to Medix2 for having reported it). Enemies could enter and then simply exit the area of truth. The PCs would know how many invisible enemies are present, but would not know where they are. In many situations, this would give invisible enemies most of the same benefits they had before (minus the ability to surprise their enemies).
On a personal note, I want to add that none of these tactics is my favorite. I suggest the latter as an alternative.
- Let this tactic work.
This is a creative and intelligent use of this spell which goes off the beaten track. Such insight should be rewarded. If your players want to spend resources protecting themselves from invisible enemies, this is a viable way to do it (and only provides the benefit of a lower level spell, Alarm, and for less time).
If you want this tactic to fail, I suggest that there should be a compelling reason (as the enemy they are fighting is intimately familiar with the way they operate).