The kit humbuckers are the standard size, so any replacement humbucker (Seymour Duncan, DiMarzio, Tonerider etc.) should just drop in. There's a caveat in that the height-adjustment screw mounting lug sticking out of the ends of the pickup are often smaller than those on replacements, and the notches in the pickup rout for them of the kits tends to match that, so on some kits (it's variable between kits) the ends of the metal tabs dig into the rout a bit and stop the pickup moving freely.
if this happens, the options are to either file off some of the metal tab on the new pickups or else make the cutouts a bit bigger. A small diameter drum sander attachment on a Dremel is useful for this.
Saying that, I had no problems with my EX-1 kit and some Iron Gear replacement pickups, but it all depends on the template the factory used to rout the cavities with. If the pickups are a bit tight, then it's not a major problem to fix.
The kit pickups often come with a single conductor + screen output lead, whilst most replacement humbuckers will come with a four conductor + screen output cable (unless they are a period-correct PAF style pickup). Some of the kits come with 4-conductor + screen pickups but it's not that consistent as to what you get.
But unless you want to add some single coil or parallel coil switching options, the connections are very similar. You might need to solder two wires together and tape them up (to duplicate the coil linking done within the pickup on the single wire version) and twist the screen and pickup signal ground wire together before soldering to the back of a pot, but it's nothing onerous.
If you choose very high output pickups, you might want to swap to a 1 Megohm audio pot instead of the normal 500k audio pot for volume, which will give you a bit more treble from what can be a quite dull sounding pickup if played clean. But that's a choice, not a necessity.
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