If it's not a consistent design then no, they need to be nuked.
Posted under Tags
kaname madou, miki saya, sakura kyousuke, and tomoe mamiya tags exist, but I haven't seen anywhere near as much consensus on their names and designs as there is with other genderswap character tags like kyonko. Homura's male counterpart doesn't even seem to have a separate tag.
There was also akemi homura (male), but it got nuked in June around the same time when Akuma Homura was finally aliased to the regular Homura tag. In terms of names, all of the tag names (including male!Homura's now-nuked tag) are derived from Pixiv (as you can see in Sakura Kyousuke's Other Name). They have a full genderswapped series tag, and even have shiptags (ex. ♂杏さや♀, shipping Sakura Kyousuke with Miki Sayaka).
I assume the reason why nothing had been done so far with those tags is because of topic #20366 concerning genderswapped Haruhi tags, though they had the boon of having generally consistent designs. If the same can't be proven for the genderswapped Madoka tags, then as NNT says.
I feel like Gomadoka has enough posts and is well known enough in the fandom, at least from my limited knowledge, that I would keep the tag to help differentiate it from other animalizations. The rest don't seem useful however.
mass update kaname_madou -> kaname_madoka genderswap_(ftm)
mass update miki_saya -> miki_sayaka genderswap_(ftm)
mass update sakura_kyousuke -> sakura_kyouko genderswap_(ftm)
mass update tomoe_mamiya -> tomoe_mami genderswap_(ftm)
Gotta do this first since a few are missing these tags.