I think there's something to this. G&L's L-series pickups are insanely hot, and the controls are unlike any other basses, with the series/parallel switch, passive bass control, and active mode without active EQ. As a result, if a player grabs one off the rack and starts messing around without understanding the controls, he/she might not dig it. Maybe there's some clipping in the signal chain, maybe it's set to active mode with treble boost which sounds a bit nutty, etc. Plus, some people think MFDs sound a little harsh. (I think this is more an issue on the guitar side, which is probably why Nordstrand builds pickups for the ASAT Special.)
But the existence of replacement pickups is a different issue. Those who actually buy the basses will typically not want to replace the pickups.
Well, as I stated, their lack of market penetration clearly isn't because of quality control or playability - and I don't really buy the premise that they stayed small by design... but I do think that there aren't enough of them on the market for it to be viable for aftermarket pickup manufacturers to make pickups for them... This isn't necessarily a slam on G&L, just the way it is... After all, nearly anyone who buys a Rickenbacker also buys them for their unique sound - yet, there are aftermarket pickups available for them...