GBA games on the EZ4 run on the NOR and PSRAM chips that the EZ4 has. To this end it really does not matter if your ?SD card is slow, they tend not to do well with those old 64 megabyte things they used to put in old phones but otherwise it is fine.
DS games on most devices do pull directly from the SD card (a type of NAND chip usually), this makes them prone to slowdown (and worse) if you have slow/high latency chips. The only reasons FAT vs FAT32 should trouble things is when fragmentation comes into play or if bad drivers for FAT were written where there are good ones used in FAT32. If memory serves though the acekard saw a bug that AKAIO could not fix and thus everybody was suggested to use FAT32 (not to mention the rise of SDHC making it all but mandatory), however I am not sure my memory serves this day (trying to recall old changelogs when there were loads of flash carts and all the reasons for said changesis hard it seems).