I would imagine the CPUs sold by Software Hut will be the plug-inable
PGA (pin grid array) type, while the A3000 has a QFP (quad flat pack)
soldered onto the board.
But to answer your question, if you did replace the 25MHz with a
compatibe 50MHz one, and you changed the oscillator for a 50MHz
version, then yes, it should run, and perform a lot better all round.
I'd also recommend getting an A3640 card. You'd just have to get a
revision which works correctly in the A3000.