Jim from WCR would know this definitively, but I think covers mute the highs "just slightly", but I dont think its necessarily in a negative way. I've heard actual PAF's both ways: with and without covers, and I prefer them WITH covers. Maybe its just the vintage mojo that goes with the covers, but I like 'em better that way.
You didnt say what kind of HB you were talking about, whether that was a PAF or a high output distortion pup, but I think the same theories apply. A distortion pup would benefit more from exposed coils than a PAF though. I think the effect would tend to be more pronounced.
As far as repro PAF's go, it seems everybody wants to "improve" them over the originals somehow, removing covers, changing something in the construction, etc:
"Hey!! These PAF's are overwound for that mega-ultra-nuclear PAF tone"...
"Hey!! WE use titanium baseplates for even MORE of that REAL PAF tone!!"
"Hey!! We use chewing gum between the coils 'cause a piece fell out of Duanes mouth into the coils once, and you know how great HIS tone was"...
IMO, as far as PAF's are concerned, there is very little room for creative license in design... if you want a PAF, build it like a PAF. Variations off the original design result in variations off the original sound. Makes sense.
Its all personal preference, but for me, I prefer covers, especially because I dont really use any pickups stronger than about 10k on a DVM, plus to me, covers just look cooler than exposed coils!!
