I am a member of a Lost in Space group on Facebook, and one of the members wrote this:
OH MY.... GOSH! So.. here I am writing a Fan Fiction Story about Dr. Smith (his beginning)... looking at a few websites... and I come across (thus far) FIVE... with the same reference/question/comment "Was Dr. Smith Gay?" ... "Yes he was.." (one site offered) " I am like.. PEOPLE where do you come up with this... this STUFF?
Because this is the Query of the Age..."Is Doctor Smith gay?". After my projectile bleeding stopped, it hit me that the reason '50s and '50s TV was so relatively inoffensive is because there was censorship, Standards and Practices, like that. You could play to Type, but only that far. He-men, prissy men, Ward Cleaver...it ran the gamut. Jonathan Harris, who started out as a Very Bad Man,

out of sheer self-preservation as an actor, began to tune Smith into more of a cowardly buffoon than a fell agent of Aeolus 14-Umbra, lest he be killed off by episode eight.

He became the priss, the fraidy-cat, perhaps from a psychotic break when It All Went Wrong and Smith was stuck on the Jupiter 2. He had manners, and liked the finer things, and I guess that's enough to get you the label nowadays.
It was not EVEN an issue in the '60s on the show. The gimlet eye of Presentism works its stupid charm on people today, who insist upon judging Then by Now.
Not an issue, period.
(No doubt you noticed how adroitly I avoided the real issue, that of writing Doctor Smith fanfic to begin with.)