1. NetScaler is sending the IPv6 packet to backend server. In response, server as expected is responding back directly to the client instead of going through NetScaler. So, if intermediary devices do not have MTU settings as per the response sent by server, then client would receive no response. Hence, you may see ICMP large packet timeout.
As these responses are not through NetScaler, we cannot really check if the response was received back by client until there is a simultaneous trace run at origin server as well.
Now, for your query regarding directing the IPv6 large packet to NetScaler would help resolving the issue or not if there is high payload. This would depend upon the MTU settings of the server or the intermediary device. If the MTU settings is high at server than the NetScaler interface MTU settings, then NetScaler will drop the packet at NIC level.