If two of those devs decided to throw their workstations off the roof once a year, would the $5000 make a difference?

Spending money you don't have to is always a bad idea, so while the unused license space may not make a huge dent on the bottom line, a company that pays attention to those things will likely outperform one that doesn't.

Not 25 devs (although that doesn't necessarily change the salary question) - if you want to go "full GitHub" and use the issue tracker for everything, you want all your staff to have access.