We are running JIRA 6.4.11 and sometimes have had sprints of different lengths because a team done goofed and closed a sprint too early (and you can't reopen it, not in our version at least )o:
If you need to calculate department metrics over teams, coordinate builds at the end of sprints and/or have team members helping out other teams, you may run into issues (we did), but nothing in JIRA itself prevents it that I can think of.
Don't think I would recommend it in a single project, however.
Just my $0.02 worth
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