57 nations with their own leagues + Utopia for 58 for sure.
I think you still get the flag of the nation the team is from, or both that and the Nations of Europe/Asia/Africa/Americas if scrimmaging a team from those leagues as for instance the team from France I had a scrimmage against last week does have the Scotland flag for playing me as well as Nations Of Europe (which they may already have had).
So if that is indeed how it works then the Nations of Europe/Asia/Africa/Americas flags are 4 more so 62, and the nations that got merged into continental leagues in season 40 are another 41 flags, so 103 in total.
Hardest minor nation flags would be Barbados (no active manager currently), Pakistan (1 active manager - last online a month ago), Costa Rica (1 active manager - last online 2 weeks ago), Tunisia (2 active managers), and Lebanon (3 active managers).
Hardest flag with its own league still in operation is Crna Gora/Montenegro (14 active managers).