It's a (weak) protection mechanism against someone who decides to flood other member's via PM. Probably not a huge concern at this site.
If you scroll down to the bottom of your list of PMs you can select a few then delete them, to make room. If you and one or two other members are involved in an ongoing private discussion that would quickly re-consume to the 50 limit, then consider exchanging email addresses and continue outside this platform.
Ironically, just today I had to do this exact thing myself, as I was up to my 50 inbox limit.
Maybe I should up it to 100. But so far you and I are the only two I know of who have hit the limit (and said so, anyway).