There are two possible ways to reach Lake Lipno (if you don't come via Czech Rep). 
When you come via Germany you must ride at least the A3 / E 56. You can leave the highway in Hengersberg or Passau and then reach Lake Lipno via the bordercrossing in Philippsreut. This may be the shorter but possibly longer way.
Other possibility is to stay on the highway till Linz in Austria and then go north and cross the border at Bad Leonfelden, this is a faster way. This is also the way for those who come via Austria. Pay attention for alcohol at the wheel. In Czech Rep. 0 % restrictively.