The stock bikes were known to be boringly reliable. It's hard to fault the bike in that pure form or restored to such form. However, hot rodding, abuse, "upgrades", modifications, and shoddy or less than proper repair work can certainly hinder reliability.
For most of these bikes there have been 30 years of opportunity for degradation, re-engineering, neglect, and outright butchering, that can make what Honda crafted quite different from when new, certainly from a reliability perspective.
Every mechanic that has worked on the bike and deviated from prescribed procedures components, can certainly contribute to unreliability.
Sometimes either "saving a buck" or masterminding an "engineering change" (whether from owner or aftermarket guesswork) can have repercussions in tow fees and inconvenience.
Anyway, if you've substituted components not supplied by Honda that fail, can you really blame the Honda design?
Honda had a pretty good recipe for making a reliable bike. Doesn't take too many ingredient changes to alter the stalwart characteristics. It's not too far off the mark to laud the design as extra remarkable because it tolerates so many hacks made to it and still provides utility, if not reliability.
It's ironic that so few like the pure stock bike, but it's that stock bike that allows them any success at all.
Cheers,