Well, the first thing I tried is to change the MTU size of the bridge. Which seems not possible.
So I digged into radvd to do it manually.
Because PATH mtu is used with ICMP the problem arises. The IPv6 client tells the webserver: My MTU is 1500 (received from radvd). So the Webserver tries to sent packages with MTU size 1500. Which is a problem because the PPPoe(WAN) interface is only 1492.
After I changed radvd to tell the IPv6 clients to use MTU 1492, alle websites are reachable again.