Largely solved but I have some witterings that might add to the discussion.
One of the more notable cases of things here was Castlevania Portrait of Ruin.
Here it was noted the game would crash and those using faster SD cards (and for many it would have still been SD, got to have that Japanese Kingston, rather than SDHC), no fragmentation (don't defrag, format and copy everything back), options to boost speeds on the cart itself, those removing audio (removes need for long reads) and more would suffer fewer crashes. Latency rather than raw read speed being the issue at hand.
Ultimately it was found to be a bug and the fix exported around various flash carts (though sometimes not for quite a while).
https://gbatemp.net/threads/which-flashcart-for-castlevania-por.343239/page-2#post-4559271 (did post the download of the whole thing around here somewhat more recently but can't find the post in a casual search, that is what most people care about though)
Anti piracy had been seen to cause slowdowns here -- if you have thousands of checks per second it can have an impact. Scrolling lists and menu timings usually being where it is most noticeable.
Various flash carts actually increased speed above and beyond what stock games might do. AKAIO (also basis for the Wood firmware) being the most noted of these but others also went there. Depending upon your point of comparison then you might have even been used to better than stock.