Haha, I started doing this with Cap'n Proto 10 years ago. :)
I periodically get crap for it but so far it hasn't really broken anything.
The biggest annoyance is exactly what you point out -- the GitHub URLs look ugly because they %-encode the plus signs. Though it turns out you can manually un-encode them and it works fine.
It breaks Make, which does not have a default rule for “*.c++” files, but does have rules both for “*.cpp” files and the older naming custom of “*.C” files.
In modern GNU make it is generally advised to disable default rules anyways. I know some people try to do portable Make, but I am pretty over that idea myself, so if I do use Make, I'm using GNU extensions and GNUmakefile.
Jokes aside though, the only major complaint people have is about .RECIPEPREFIX, which I also don't follow. I didn't read too many comments, but the top voted comments do not appear to take issue with the advice to disable built-in rules.
I'd be surprised, since it is far from the first time I've heard that advice, and it never seemed very controversial.
(In my opinion objectively the worst possible choice because + requires URL encoding ;))