I have been inculcated in Trek literally my whole life. My parents were first-generation Trekkies, and so the reruns were a weekly part of my existence from before memory. It took longer to latch on with me than Star Wars and Transformers. I didn't dislike it, but it required more attention and active thought than elementary-school-aged me could muster. It started clicking around the time I was ten, and rapidly carried me away. Star Trek IV came along when I was twelve and knocked me over the ledge that I was teetering on into full-on Trekkie-dom, and TNG premiered the following Fall, which squared and cubed it for me.
And, because my parents are engineers and I inherited the hardwiring that leads to that, I've skewed hard toward the technical side of things from early on. Logistics and engineering and timeline matters and science and all of that -- I'm in there.
I've spent the last three-plus decades figuring out how to make things work, how to make them fit... I've used proper research methodology when those working on the shows and movies haven't, and come to evidence-based conclusions that clash with official lore. I've made almost everything work, sometimes even when I have to close one eye, tilt my head, and squint to do so. One of the things I always hate to do is give up on rationalizing or retconning something, and just acknowledge that the writers didn't know -- or care -- what they were doing.
So recognize how hard it is for me to say this: V'Ger, the Whalesong Probe, and the Nexus make no sense.
V'Ger, in the original version of TMP, was generating an energy cloud "over eighty-two AUs in diameter", with energy readings almost off the scale. That size got scaled down somewhat in the Director's Edition to "merely" over two AUs in diameter. They tracked it moving from Klingon space into Federation space on "a precise heading for Earth". But the whole time it was, as you said, moving sublight. No indication it was warping space or tunnelling or any sort of go-faster tech.
The Whalesong Probe also was not moving FTL, for the Saratoga to intercept and scan it. When the ship had its power knocked out and started drifting, the Probe was still poking along -- it didn't immediately zip off at zuperluminal velocity.
Both of those were presumably making their way to Earth from wherever for over a century. The race that sent the Probe needed the lag time for the outgoing whalesong to stop reaching them before then sent it. And we don't know how long it took the "machine planet" that found V'Ger to build that ship around it and sent it back where it came from.
The "Solar Neighborhood" is roughly five hundred light-years radius from Sol. With the exception of Rigel, all the individual stars we can see are closer than that. FJ took a lot of that into consideration when he did his Technical Manual in the '70s. Greg Mandel likewise when he did his Star Charts. The fact that Rigel is so far away presents problems I won't get into here. But that means if V'Ger and the Whalesong Probe were traveling sublight, they could only come from a couple hundred light-years away, at most. And the fact that none of the races we know seems to have ever stumbled onto those planets is a stretch. But it could happen. They're just problematic as hell.
The Nexus is far, far worse, though. It circles the galaxy every 39.1 years. Which means, with the circumference out around where we are being about 314,000 light-years, the Nexus is booking it at about 8,035 light-years per year -- or warp 9.99, TNG scale. While it was certainly energetic, it also wasn't moving faster than light any of the times that we saw it. I highly doubt it would slow down when people were about and then piff off again at ludicrous speeds.
