Yes, a zoo hypothesis is much like a simulation hypothesis, and the data we use cannot exclude it. (Nor can they exclude a simulation hypothesis.) We choose to assume that grabby aliens change their volumes in some clearly visible way, exactly to exclude zoo hypotheses.
If we are inside the colonisation volume, its change will be isotropic and will not look strange for us. For example, if aliens completely eliminated stars of X class as they are the best source of energy, we will not observe it, as there will be no X stars in any direction.
Not a cosmologist but I'd guess that there are enough weird unexplained phenomena in cosmology for it to be possible for aliens to hide in them, or, for us to have just rationalized them away as natural phenomena with fake cosmological theories.
The crux of this, for me, is whether it's physically possible to do the stuff you want to do in the colonized universe (dyson swarms, etc) without a zoo civilization of our level of development being able to see it in our telescopes.
I imagine the construction of a firmament screen, a cosmic-scale device surrounding us with a false image of an uncolonized universe, we might be able to argue that the firmament screen is physically impossible (or absurdly difficult to justify the cost of) even with superintelligence. If an astrophysicist could make that argument, that would rule out the zoo hypothesis for me.
I guess they wouldn't need a firmament if they were doing a thing where.. they just let life-supporting planets see them until intelligent life emerges, because unintelligent life would be indifferent to them, and then once intelligent life starts to build telescopes they descend and scan everyone and move it into a simulation. This would get them a completely accurate biological history. The simulation, from then on, might not be completely accurate, but if so, I am not sensitive to what would be missing from it.
Robin Hanson created a model of grabby aliens. In this model, we live before the arrival of an alien colonisation wave, because such a wave will prevent the appearance of the new civilizations. Thus, we could find ourselves only before the arrival of the aliens if any exists in our Universe.
However, at least some of the colonisators will preserve a fraction of habitable planets for different reasons: ethics, science, tourism, neglect. Let’s assume that it will be 0.01 of the total colonized volume. The numbers could vary, but it still looks like that in a densely packed universe the total volume of colonized space-time is significantly larger than the space-time for habitable planets before colonization arrival, and thus even a fraction of this volume could be larger than the volume of the virgin habitable space. This is because the colonized space will exist almost forever until the end of the universe.
Moreover, any small effort from the alien civilization to seed life (artificial panspermia) or to protect habitable planets from catastrophes like asteroid impacts will significantly increase the number of habitable planets inside the colonization zone. Hanson’s model also assumes that the probability of civilization appearance for any given planet is growing with time, so later regions will have a higher density of habitable planets, as more planets will reach this stage.
Given all this, our civilization has higher chances to appear after the colonization wave has passed us and thus aliens need to be somewhere nearby, but hidden, which is known as the Zoo Hypothesis. In other words, we live inside the sphere of influence of Kardashev 3 civilization which either helped our appearance via artificial panspermia etc or at least do not prevent our existence.
In this formulation, the idea starts to look like a variant of the simulation argument as here it is assumed that an advance civilization could create many non-advance civilizations.