A2000 don't, but yeah A3000 and A4000 have a 50mhz clock on the motherboard. I'd assumed it was used for something else, but it could limit access to 25mhz. There is a clock source jumper, but I don't know what it's for.
Sorry, I always forget 2000's as a "big box" since they are essentially glorified A500's.

I'm 99% sure it's a 25MHz on the motherboard. Lots of 040s have a 50MHz because that CPU double clocks, but I'm not aware of one on any motherboards.
The clock jumpers determine whether the it uses the clocks from the motherboard or the ones on the CPU card.