I love SBC's. I originally got into them because I don't have a lot of space for retro computing and realized I could build a compact retro system on a small ISA backplane and a half size SBC. I now have a small collection of components. I think one of the coolest things is being able to switch to a different generation of PC by simply swapping out the SBC. I don't need a wall of beige boxes; just 1 case and a storage bin with ISA cards. I make sure to get SBCs with integrated I/O and VGA, so for a basic system I only need 2 ISA slots: SBC + sound card. Also, many SBC's come with a DOC (Disk on Chip) socket, which you can use for an XT-IDE ROM.
SBCs were put into equipment that had a much longer service life than your typical consumer PC did in the 90's (like 20 years); SBC's with 486 CPUs were manufactured until about 2006. Chances are good that the RTC battery is still good. I haven't had any issues with mine.
Industrial computers don't have to be expensive. Just keep an eye out. Last year I bought a P1 MMX 233 half size ISA and a couple years ago I bought a 486DX133 half size ISA. The pentium was $100 and I don't remember what the 486 cost, but it was definitely less than $100. I find that it helps to figure out exactly what you want until you've narrowed it down to a particular model. That's usually when I have some luck finding a good deal. Don't be weary of getting one from overseas either. That's where a lot of these industrial PCs were used in the first place. I also strongly recommend only buying boards that you can find manuals for because things like jumpers and headers are frequently not labelled.
For my application, backplanes are pretty cheap. I have a 2-slot and a couple of 4-slot backplanes, and the most I ever paid for a backplane is $35 + shipping. That was a brand-new 4-slot ISA backplane that I bought directly from Advantech (I recently scored an Advantech case for $70 in really good condition, and did not want to modify it to fit the 4-slot I already had). So, again, just keep an eye out and it's possible to find a good deal.
That brings me to what I think is the biggest challenge with industrial computers: the cases. Industrial computer cases are super expensive, and for good reason; they're usually very high quality and built out of heavy gauge steel. Also, many backplanes don't follow a form factor standard. Mixing and matching backplanes and cases usually results in mounting holes not lining up. If you don't mind spending an afternoon with a drill, grinder, and ruler, it's not a big deal. (I probably don't have to say this, but please don't hack up a vintage case). If my goal wasn't to build a tiny computer, I think I would have just used a standard ATX case and modified it to fit whatever backplane I ended up getting. Instead I decided to DIY a case until I found that 4-slot Advantech case for $70.