If you look inside the A-S3000 you will notice the massive heatsinks go almost all the way from the top to the bottom so they clearly realised the heat that would be generated. Someone reviewed one of their other amps, the 2100 I think and they measured that even when idling it used around 70w of electricity and hour so if you think of a 60w lightbulb for example and how much heat is generated it probably explains why they run warm and also while even running them hard they don't get much warmer, in a domestic environment anyway.
Another thing of course, while we all want our kit to last for decades, the manufactures give for example a 5 year warranty on these so they probably think if it lasts at least that then it's job done. Another good friend of mine pointed out that in reality we often change our kit long before it wears out. I know in the past I've had kit where I wanted it to last forever and then changed it shortly afterwards!! Although if look at some of the other famous Yamaha amps from yesteryear they are only really now needing a recap after 25 years or so.
Having said all that I would certainly buy another Yamaha amp in the future, no question. This amp gives me everything I want and more, I've owned more big name brands than I can think of and they've all had their quirks and faults.
Impresses me every time I look at the internals! A re-cappers nightmare though I would think, like most Jap amps!