I can't speak for every owner, but I can share personal experience of mine and a friend that I think it anecdotal about FJ40 purchases. I am sure a lot of people buy 40s to flip because the market was hot, is still kinda hot, even as the focus shifts to later LCs. So yes, there are a lot of speculators in the market. Last question first - YES, be wary, or at least educated in looking at 40s. I can't assign any exact percentages, but some are candy coated trouble, some are flat misrepresentations, and some are genuine peaches. They're all out there.
I also think that some people buy 40s with the intention of keeping them and quickly figure out that FJ40s aren't their cup of tea. You've read over and over they are small tractors and that is a fair comparison - they are stiff, ride like they are stiff, can have bad steering habits if not maintained, are powered by a 6 cylinder Chevrolet inspired power plant from the 30's, are prone to rust, should be sold with hearing protection, and generally feel like riding a roller skate at speeds above 50mph. Lots of folks fall in love with the idea of an FJ40 but once they own one find out they don't necessarily like FJ40s.
I love mine, but I'll admit that there was a short period of time I entertained the notion of selling it because I wasn't sure how I was going to enjoy it and justify owning it. After a while I came to appreciate it more and found it to be the inspiration to undertake a few new activities - now I wouldn't part with it. I also have a friend from church who was hell-bent on owning one so he went to Mecum and bought a fine, and very expensive, example. Within a year he was sick of it. He complained it was slow, rough riding, underpowered, and crude. I don't know what he thought he was buying - but he CLEARLY falls into what I think is a sizable subset of 40 owners: people who love the idea, but not the practice of having a 40.
You'll have to talk to potential sellers and glean from their stories which camp they are in.