If your initial Passenger Ship designs didn't have FLT drives, it's very possible that they were on their way to another star system with their migrants on board. They may never have been able to arrive at a shipyard to upgrade for the remainder of your game. Take a look at your old save and see where they are located and where they are heading.
I checked that yesterday, and indeed, many of them were unfortunately in deep space, no doubt doomed by my inexperience to remain useless for the rest of the game. However, some (presumably recently created) were still in my home system, and they exhibited the same refusal to accept a queued retrofit command.
Passenger ships aren't covered in detail in Timotheus' guide, but the "we're missing a critical private design" pop-up appeared early on and suggested it was vital I create a passenger ship design; still being very new to the game, I created it before having FTL tech and without paying close attention to the Design pane automation settings.
I'm much more experienced now compared to when I began, since I've finished that entire game, although I rushed through it and ignored some finer details. Today I've mostly just been reading the Galactopedia or, when it lacks detail, using a search engine to fill in the gaps.
Thank you all for the advice. I've been playing 4X since the days of MoO/2, SMAC, the early Civs, and all that jazz, plus many (so, so many) that didn't quite live up to the MoO legacy. A few were pretty good (GalCivII for example), but Distant Worlds is the first space 4X to release this century that feels worthy of the MoO mantle in its way, despite some of its flaws. It's been on my Steam wishlist for years now, and I'm very glad I decided to get it (from GOG, since their sale brought it back to my attention).
It's a shame the DW community is so dispersed, but you can only play even great games for but so long before your attention moves elsewhere. That being said, every now and then when the topic of comparing 4X games comes up on some Steam or Internet forum, occasionally DW is mentioned, and always as being superior to the more recent/flashier games like Stellaris and Endless Space 2.