Well technically fragmentation can happen in IPv6; This is the wikipedia article on it.
This Juniper page is a bit old but it shows that you can clamp an MSS for TCP over IPv6 on Junos the same as you would in IPv4 using the same command,
tcp mss. The same is shown in this article for Cisco IOS 15, using the traditional ip tcp
So you can configure MSS clamping if PMTUD isn't working as it should be in a part of your network, otherwise, you should be ensuring that you are aiding the smoothing running of PTMUD across your networking so that MSS clamping isn't required (I understand this isn't always under your control).
Here is a link to a newer Junos article for Junos 10x rather than 9, I can't find one for 11 and I'm not in front of 11 right now, but I expect it will be the same.