I always assumed that Yoda knew Anakin because of his dialog in TESB. In TESB we learn the following, Yoda was a Jedi Master. He trained Obi-wan. He knew that Luke’s father was a powerful Jedi. He saw much anger in Luke, like his father (and then Obi-wan commented that he hadn’t been so different). In ROTJ, Yoda says there is another Skywalker (pending any new info in VIII or IX, that has been assumed to be Leia). So Yoda shows great familiarity with who Anakin was and is. It has never seemed far fetched that Anakin would have known him. His absence from any of Vader’s dialog has always indcated to me that he thought Yoda was dead - only Kenobi had been left to train Luke. The explaination I’ve always accepted, that I think was used in the EU, was that Yoda chose Dagobah because of the dark side cave (a place of evil it is) that could mask his presence. Someone posted above that Frank Oz always thought the character was more refined and on Dagobah in exile. Not only does that jive with the PT, but with what I had assumed prior to TPM.