While there are differences, it's really hard to make sweeping generalizations. EMG PUPS are active- and sound great to me when they feed a passive cicuit. Do they sound as good feeding active citcuits? A lot depends on the circuit. My experience is that a cheap active circuit is only a a sales tool ("Hey, this one's ACTIVE! So, it's worth more money!!") and you'd be better served at lower price points getting a good passive instrument.
Good active PUPs can be tailored to overcome some limitations inherent in magnetic pickups. To get more output you need more wire, but that chokes the highs. So, you can design a PUP with low output but a wide frequency range, and you can make it a noice cancelling PUP, then put a pre-amp in it to boost the signal back up to a useable level, and shape the sound with the pre-amp. That's one way to get a noisless Jazz bass for example.
But passive PUPs feeding good active circuits are very good and very useful. In fact, that's the most common active set-up. Why? Because it offers tonal flexibility, and it offers lots of the advantages of active circuits (impedance buffering, more output, tone shaping, etc.) with the ability to build that basic sound from a classic PUP. Plus, you CAN give it a passive option (which may or may not be useful- depends on the design of the passive section*). Whether one is more useful for you depends entirely upon YOUR needs and your prejudices.
*Most of the passive options I have experience with are really just an "OOPS! I was too lazy to change my battery and the pre is going dead on stage!! option. I know Sadowsky offers a passive option that not only by-passes the pre-amp, but sends the output to a regular passive treble-cut tone control. That's not the same as the passive option on my Laklands, where the passive swtich just by-passes the entire pre and sends the PUPs straight to the PUP blend control.
jte