The running theory is that there was a dispute between the Astros and Monsanto (the makers of Astroturf) over the use of the term and trademark for "Astros." Not wanting to get caught up in the dispute (and/or possibly to comply with an injunction that issued as part of the lawsuit), Topps produced the cards without the logos and referred to the team as "Houston" on the cards.
https://www.net54baseball.com/showthread.php?t=181662
https://www.thenationalpastimemuseum.com/article/great-topps-baseball-card-monopoly-part-6-conflict
There is, however, some question to the validity of this story as it has never been officially confirmed by Topps.
However, it's been noted that Fleer also omitted the Astros from their '67 and '68 cloth sticker sets. In my opinion, both companies leaving out the Houston team logos from their sets in this timeframe points to something more broad affecting their decision.