Normally, a good, mature solver should provide functions to simplify / optimize the input structure.
When I worked on our solver, we came up with quite elaborate and refined via merging functionality.
Via merging is a standard step in parasitic extraction tools, and in some EM field solvers (like EMX).
I am surprised HFSS does not offer easy to use functionalities for that.
The most direct way to figure that out is to ask Ansys support.
But be cautious - replacing via array by a large slab of metal may incorrectly allow a lateral current flow in your simulations, you should make sure this is not happening in simulation.
Your solver needs to comprehend that, and distirnguish from a real slab of metal (some vias are made like that).
There are other operations that may be highly beneficial to simplifiy the GDS geometry, to enabel small-size mash for simulations.
One of them is polygons having too many points. For example - a circle defined by thousands fo points.
This may (depending on solver) lead to huge and unnecessary mesh size.