yeah this is a side-effect of the fact that hax 2.5 handles some stuff (APT) properly where 2.1 completely ignored it.
as stated in the tweet, all devs have to do is rebuild their app with latest master ctrulib and add osSetSpeedupEnable(true) to their initialization code. they can also toggle the speedup at any time with that same function. (people could make a battery-saver mode for example)
i tried to make sure people who worked on performance-critical stuff (so emulators for the most part) like endrift, aliaspider and staplebutter updated their stuff in time for 2.5, which i believe they did.