Will they be affected: Yes. They should (but probably won't) update their installers. They all use the same dll files, though, so if you install the new versions using the 3.999z2 or 4.90 installers, you have fixed the problem for everything at the same time.
When you use an FSUIPC installer, that checks and will only overwrite the dll if the installed version is older than the one being installed - for instance, if you install 4.90 today and then install the Blackbox Airbus Prologue packs, the version of FSUIPC in the current versions of the BBS packs are older, so will not overwrite 4.90. If the package just copies the dll file in, however (which they shouldn't!) then that could be an issue. That's always been the case, though, unfortunately.
Cheers,
ian P.