To register an NPAPI plugin in the system, I have to add the path to it to HKCU/Software/MozillaPlugins. If two versions of the plugin DLL for a specific MIME-type are registered there, will the newer version be always loaded? Or the version is irrelevant and it is not known which one will be chosen?
For all intents and purposes the answer to your question is undefined, since different versions of FireFox will behave differently. The most important bit is to simply not allow that to happen =] If you set things up right you shouldn't be able to have multiple versions of your DLL registered there, though I guess you could have one in HKCU and one in HKLM, in which case there is not guarantee that it will behave the same on each browser.
I could speculate based on experience as to what would happen, but the important thing is that you need to avoid it; as an example, FireFox 3.5 changed (without any warning or notice on the changelog) the way that it detects plugins from what Firefox 3.0 did -- because both more or less followed the guidelines.
The other weird thing is that many versions of Firefox will actually find all plugin .dll files in the directory of the file referenced in the registry key, not just the file you specify. For this reason (and because which version it picks differs by version) we always install the plugin into a version-specific directory, such as 1.1.0/npMyPlugin_1.1.0.dll