I've always imagined that Vader assumed that if Yoda was still alive, he would be on Alderaan with Bail Organa, as he helped Yoda escape - so he would consider him dead. Palpatine clearly saw that Yoda escaped alive, and made no further attempts to hunt him down and destroy him... Maybe he knew that as a CGI character he could fight back, but as a Frank Oz puppet he could only speak and use the force to levitate things!

Regarding the "Obi Wan has taught you well", I always thought "well he didn't say much to Luke", but he didn't know about Luke's trainning with Yoda. Not much of a plot hole, but a gross missasumption by Vader, even considering Obi Wan was killed by himlself years before ESB.