For starters, like you say, the input for Hooligan Combination could use some simplification. The unorthodox command lends itself to execution errors if you miss-time the punch button press.

Spider is easy to perform, but the spacing is key, and depending on how you code the hitboxes it may end up being not too safe or abusive, like you fear.

in some kof games mary has both the grab (qcf+P) and the overhead kick (qcf+K) which is what lead to some mind games (and you also have to add her slide CB,F+K to it)  the grab by itself would be pretty useless otherwise.

Hooligan is not useless at all, usually depending on the game.  SF5 did simplify it's command but it's also a bit slower to fit with the system.  On the other hand you can use it in sneaky new ways that you couldn't before.

I've never played a KoF game with Mary in it to compare.

Though I've always performed Akuma's Demon Flip as opposed to Hooligan Combo.