None of the complaints commonly raised against akali or kat really have to do with them being hybrid, so much as them being able to deal tons of burst damage with resets and high mobility. I don't generally have issues with them, but people who underestimate their burst and let them get the resets can get understandably frustrated.
As for hybrid champs as a whole, that is a huge can of worms, but it basically boils down to most hybrid champs don't build hybrid, they just build the one damage type that best suits their kit. Akali and kat usually build full ap (plus gunblade sometimes) because their kits work best in burst combos. Jax usually builds AD over AP because his half of hit kit stems around getting in as many autoattacks as possible. Even champions like Evelynn who can build hybrid and do well will benefit more from focusing on a singular damage stat, just because AD and AP have stats that multiply their effectiveness (crit and AS/CDR and rabadon's passive) but they don't scale off of each other.
So hybrid champions aren't bad by any means, but the current state of the game makes specialization more powerful than versatility.