It's a good suggestion, but Messenger Plus! won't use them anymore, so you may modify them yourself without causing any malfunction. Thi way you could store them in a password protectes ZIP or RAR file. Or even move them to a private folder in XP.
As Archive, Messenger Plus! doesn't use them anymore (that's why they're archived). Anothe problem would be to encrypt 2 years of logs, that can be challenging for your computer and for MP!. It could easily cause your system slow down dramatically for a while, and probabilities of file corruption would increase.
My advice: Turn encryption on and move the archive somewhere else if you don't want others to access it.