Will the brass from the PMS have any effect on the EMG pickup?
Depends on which model of pickup.
EMG's active humbuckers and P-90s are thickly insulated on the sides, so any material placed around the edges won't affect them. The underside and top are not as protected, and something like a
large brass plate underneath the pickup could
potentially alter the tone in the same way that the baseplates on Telecaster bridge pickups do, or the top reflector plates on firebird pickups. (In fact several EMG active pickups are constructed like firebird pickups, and an additional brass plate on the top or bottom could affect them greatly.)
EMG's active single coils and mini-humbuckers aren't as insulated on the sides as the larger pickups are, so material
adjacent to them can potentially alter their tone, in addition to materials placed below or on top of them.
EMG's passive pickups, of all kinds, are not insulated any differently to pickups by any other manufacturer, so anything which works for brands like Seymour Duncan or DiMarzio will work just as well for passive EMGs.
I understand the EMG pickup isn't affected by vibrations from the wood.
It is, in a senses, a self-contained unit.
This is not true. EMGs, of all kinds, are just as affected by the vibrations carried through the wood of the guitar as any other brand or equivalent style of pickup is. The tone of some of their active designs, especially their active single coils, can be
more directly influenced by the construction and materials of the guitar than common passive equivalents. In some extreme cases, harsh vibrations can carry through the pickup and be audible in the signal as a very low rumble or a very high scratching noise, similar to how unpotted passive pickups can be somewhat microphonic.
As a general rule of thumb, EMG pickups use weaker, more sensitive coils and/or weaker, more sensitive magnets, then you'd usually find in equivalent pickups from other brands. Most of their pickups use massively mismatched coils to maintain a broader frequency response and produce a more dynamic and sensitive signal. (A few of their humbuckers do use more regular, closely-matched coils.) This is very important for their basic active designs, since the nature of the original preamp will cause a certain amount of compression and limitation to the dynamics, so starting with a more dynamic coil configuration in the first place helps balance the sound. (This is not as necessary when running the pickup at 18v, or with the later 'X' preamp, which has more headroom.) It is in fact
because the coils and magnets are so weak and so sensitive that the pickups then have to be fully insulated and have their output brought back up by a preamp.
Or to put it another way, inside an EMG active pickup is, essentially, an extremely low-power, extremely clear, extremely 'open' pickup which is closer to an acoustic or floating jazz pickup than it is to a regular electric guitar pickup.
With that in mind, the construction of the guitar and how it resonates absolutely
does affect the sound you get from an EMG active pickup (or any other brand of active pickup) and you should not treat them as any less sensitive than you would a common passive pickup.
All that said, wood mounting a pickup very rarely has any audible affect compared to pickguard or ring mounting the same pickup on the same guitar. I've done the conversion on probably a dozen guitars, both top to wood and wood to top, and I can only think of three times when there was an obvious change in sound which could not be attributed to any other factor. One of those times was with active EMG 60AX humbuckers, which took on a duller sound after I changed them from wood mount to being hung from an added pickguard; the other two times I can think of, I moved passive pickups from pickguards to wood mount, and they got brighter. But I've done it many other times where there was no discernable change in sound at all.
In terms of safety and durability, I've not had, seen, or heard of a pickup ever being physically damaged by being wood mounted.
I've called EMG many times to ask them directly, but they never answer or call back.
EMG have been backlogged for about three years now and their staff are all busy every second of every day. As Tony says, they're not actually a a very big company, and in fact in many ways they are now more 'boutique' than brands like Bare Knuckle, for example. Other than a couple of their most common models they keep regular stock of, EMG pickups are pretty much made-to-order, and these last few years of supply chain problems and everyone bored at home wanting to make, modify, or just buy new guitars, has put a lot of stress on these (relatively) smaller companies.
Right now I have an order with EMG for some custom switches and pots, two regular pickups and one with a modified magnet. I've had that order with them for four months now and I do not expect to recieve it until the start of next year. That's the estimate they gave me when I made the order to begin with, and in my experience EMG's estimations are accurate. In past years they've turned pickups around to me, including international shipping, within a month; now, six months+ is common for really custom jobs. That's just how it is now, and will continue to be until they have caught up with the backlog.
You may have noticed this is also why Warmoth has stopped offering certain options, such as white paint.
If you need to talk to EMG, I recommend e-mailing them instead of phoning. It's easy for someone to not hear the phone ring, but they will see every e-mail eventually. It might take them a few days or even a couple of weeks to reply, but you will get a response.