There are several forms of 'protected' pbo
the first type is a misnomer in that *some* of the files within *might* be raPified. This was formerly known as encryption in the early days when people, naturally enough, mistook BI's binarised mission.sqms and config.cpp's as having some sort of encryption or protection. The ofp engine raPifies all sqm and cpp files before it uses them, so pbo content containing bin files, are simply that process, pre-empted. Plenty of tools available (mine or others) to raP and DeRap.
The second form is compression, or run length encoding, and in no way is intended to protect anything. In fact, it's use is frowned on by Bi as slowing the engine unecessarily. It is not present in elite, and wont be present in ArmA (safe bet). There are tricks and traps which *could* be utilised in the decoding of a compressed file, but to date (5 years !) I have not seen them intentionally employed except by accident by some very very poor early pbo tools. Plenty of good tools available, including mine, that resolve this 'undocumented feature', and it is highly unlikely anyone wishing to 'protect' their pbo will get away with it using this method.)
The 3rd form is a rather nasty trojan inserted by amalfi in his very popular (and very good) makepbo / unpbo tools. I can't recall offhand the name of the protected filename, not important, but, if someone attempts to decode a pbo with this filename present inside it,,,,,,, This 'method' is specifically employed by ags addons to name one. However, later tools (mine, and from memory, pbopatcher09, winpbo) all resolve this issue.
Another form of protection is to case sensitise the filename and or extension. Certain pbo tools, winpbo in particular, an excellent gui type, fall over with mixed case names, as does coc's binview (a separate issue, but same story)
The final form is particularly unpleasant and was enhanced by our Russian Komrades (OWC / OWP). The header of a pbo file contains reserved fields. Most, nearly all, pbo extractors expect these to be as nature intended, eg, aka bis. Any deviation, they fall over. So far as I know, my DePbo.dll is the only one that can cope with this wrinkle. Other tools may have followed on after I released the information. There *are* pbo's that have incorrect header info, caused by poor tools, but they aren't intentional. The Comrades elevated this to an art form.
If you really do want to go down the tunnel of protection, this form of protection is the only one currently that has a half-hope of succeeding. You'll have to visit the pmc forums (necromatix.com) to get further info. Download one of the troublesome addons and my tool, and you can 'see' how to do it. It involves a lot of stealth and jiggery pokery with pac/paa files and a few other things. But, if your determined.... (so am I, to break it)
While I can respect your wish to protect your intellectual property / your creative effort, the thing you learn real fast about this odd communtiy is it's share nature. We're all here, and have been here, for many years, pushing the envelope of what we can do with this fabulous engine. No one, so far, has benefited much by keeping stuff to themselves. In fact, if it weren't for the generous nature of the early pioneers, we wouldn't even have pbo tools, let alone scripts and all the other 'ways' of doing things. You should consider, that someone, somewhere, is going to learn something exceptionally valuable, just looking at how you did something. we all benefit.
Finally, if your interested, ArmA will undoubtedly contain protection in the form of what bis are touting as 'certified addon developers'. I have no inside knowledge as such, but it will be a safe bet this 'certification' will take the form of a unique key signature, identical to that employed in Elite.