You should upgrade from 5.0.6 to at least the current version of 5.x, since there were some security bugs fixed in the interim.
ZCS 6.0.6 has
some bugs. The only question is whether there are any bugs relevant to you. pm.zimbra.com is helpful here. (Look at open issues in GnR, as well as any issues that are fixed in versions later than 6.0.6.) You can also search bugzilla.zimbra.com to find bugs that are reported for specific versions--although it's not exactly easy to find a bug that was reported under 6.0.4, say, and then fixed in 6.0.5.
As for me, I'm happy with 6.0.5 (after upgrading from 5.0.20) and will skip 6.0.6 due to
Bug 45906 - Junk button not working correctly.
One major issue to watch out for with 6.x is the
change to default backup behavior in Network Edition. But since you use FOSS, that doesn't concern you.