+1 on putting EMG's close to the string. There's no reason not to run them high, they're made to be used that way, and compared to passive pickups, there's much less "string pull" from the magnets.
That said, the active J's do have the lowest output of all the EMG pickups I have tried. There are passive P-bass pickups out there that are louder. When I tried mixing the J's with other EMG pickups in the soapbar format (DC, CS, TW, and P5), I couldn't get a good level balance without adding a booster.
Adding EMG's PA-2 booster amp is quite simple, and if you still need more level after raising the pickups, that's a good option. You don't have to drill holes in your bass- I set the switch on mine to be always on, taped it up, and stuffed it into the control cavity.
On the other hand, if you're using the J's in matched pairs, why worry about it, unless you need more level to drive a tube amp into distortion? The EMG's are extremely quiet, so RF noise and hiss shouldn't be a problem.
BTW, one of the upsides that I noticed with the low output, was that it left lots of headroom. With high-gain amps like the Orange Terror Bass, that can actually be an advantage...