Some inconsistencies with the mirror maps have come to light. Specifically, by default, mirror maps are played with new creature banks (see the manual for details).

What nonsense is this? New creature banks are only associated with mirror maps through joint installation. Any map can be played with them, whether it's a mirror map or a regular one.
Yes, the h3dm1 map is traditionally played with new creature banks because it usually has many hives, and playing with old creature banks is less interesting.

On other mirror maps, there isn't enough of a difference to talk about any established rules. In my opinion, playing on any map, including non-mirror maps, is more interesting with new creature banks.
It should be noted that the increased strength of guardians in the new creature banks does not allow them to be fully utilized on maps that are not rich in resources and have a lot of contact between players. Therefore, for example, it makes no sense to play Hypercube, whether it's a mirror map or a regular one, with new creature banks.

But you were right in suggesting that the mirror Hypercube should also be played with new creature banks :) Only for this, it is necessary to reduce the strength of the guardians specifically for this map, which is technically not difficult to implement.