There is prolly nothing wrong with pausing, I just have never coded one for a game.
Two ways I could make a pause that I can think of fast, first: Deactivating everything but then menus would not also work until unpaused.
Second: adding a deactivate function to almost everything then it would trigger when paused but would not affect the object handling menus etc.
Bad thing about the latter one would be that it would add a ton load of more extra work, first option on the other hand could be done in few minutes.
Never done a pause also did not see a reason to have one in this game but if you all want one I will add it.
EDIT: Also game up with a third idea that is prolly used in the other metroidvanias konami has made, still very laborious method.
Save the current game state, go to a different level that has the menus filling the whole screen, then when done selecting or what ever return the game state and leave the menu level.
At least this is how I imagine Konami's metroidvanias would work.