Point taken

In-game hooks, in terms of sd2snes lingo, are a means of periodically stealing a bit of the SNES processor's time while the game is running. The purpose of this is to carry out extra tasks, such as RAM patching for certain cheat codes, and querying the controller so you can use button combinations to reset the game, go back to the sd2snes menu, etc. without having to get off the couch =)
They work similar to the more advanced cheat cartridges of the time but are far less disruptive. Nevertheless some games have issues with them because they have very tight timing.