The question was: Should alien hyper modules be changed? How?

NO - Hypermodules are fine the way they are 36%
Hypermodules should add pollution 27%
Hypermodules need a boost! They are too weak! 16%
Hypermodules should level up slower 14%
Hypermodules should give less productivity 5%
Hypermodules should give less speed 3%
Hypermodules should require more energy 0%

These results suggest that most users want a nerf of the hyper modules (27% + 14% + 5% + 3% = 49%)
some want even stronger hyper modules (16%)
and some want to keep them as is (36%) - this was the single choice that got most votes.

Looking at these results i have decided to make alien hyper modules add some pollution per level, users of hyper modules should be happy because it can be useful to attract even more biters to your base which then can be converted to precious alien ore.

The balance change will come after or with the release of 0.17 and the most likely necessary update of this mod.

How about making it an option in the config?

Something like:

Hypermodule pollution modifier per level: 1
Hypermodule energy consumption modifier per level: -1
Hypermodule productivity modifier per level: 0.5
etc...

Should be possible to go from -5.0 to 5.0 per stat (values in percent), so people can disable/enable and rebalance to their liking, because while I think its great to have a late game scaling module, it also needs to have downsides (pollution, energy, etc)
So you can always enter a negative number for a smaller modifier (less pollution, less energy consumption, less productivity, and so on) and just 0 for no scaling at all (i.e. no modifier on speed) and a positive number for a greater modifier per level (the way it is now)

But that's just a small idea, great mod either way.