Firstly, these maps should have negligible fps impact. If you read the description, they are NOT applied as textures, but as mathematical processes to the base texture, pixel by pixel. The 4.0.0.2 Nif engine seems to be able to perform these operations without issue. The overhead seems to be more buffers allocated and some extra maths!
Secondly, the extra maps needn't be the same resolutions as the base map. The engine scales them up so long as they have the correct proportions. e.g. you can have a 1024 base texture with a 512 or 256 pixel glow map. Doing this reduces the size of the mod and disk space consumed, though not I suspect memory usage. You need to experiment. Sometimes using a reduced resolution effect map looks a bit shoddy.
Finally, if a mesh supports a map you don't need, 'deactivate' it with a really small texture of the type that produces 'no effect'. An example would be if you don't want to use a glow map, use a 32x32 pixel 'solid black' glow texture.