First off,
Lou Wagner was either 18 or 19 when this episode was filmed.
Second, while there may have been veiled references to homosexuality on other 50's and 60's shows and movies, I am pretty sure this was not one of them.
I think if
Jonathan Harris had any inkling that future viewers would have seen his character that way, he would never have played the scene the way he did.
This was just more Dr. Smith silliness. If you see something darker, that is you.
Over all, the episode was more rounded in terms of giving everybody something to do. Judy got to help out on the controls after the first liftoff, and Penny played an active part in much of this episode. There was also a lot less overall silliness, and more straight story.
btw, I think this is another case where LIS got to something before Star Trek - At one point the Zaybo, which had been either a lion or an invisible cat-like creature, is played as a human female. This is ahead of the scene from
Assignment: Earth (1968), where Isis the cat takes human female form for a few seconds near the end of the episode.
One other thing - I think they may have re-shot the scene of the Jupiter 2 leaving F-12, not re-used it from
Wild Adventure (1966). The bottom of the Jupiter 2 is shown as two-tone, which I do not remember from season 2. Of course, it could just be me.