If you rode on the wheels for a while with the bearings loose or with the grease washed out, the races could very well be pitted or scored. I don't know anything about your wheels, but unless they're pretty expensive, it's likely to be cheaper to replace the whole wheelset than to rebuild them with new hubs. BUT, they can't know the condition of the races until they pull the bearings. Have they already done that, and now they're telling you that the races are junk? Or are they just telling you that by external inspection (I wouldn't trust that).

A CX bike ought to have hubs that can withstand flowing water you'd think, but I don't know anything about that. In the kind of conditions you ride in, it's a good idea to check all your bearings for tightness every year, and get fresh grease in them every couple of years, or get your LBS to do it.

Chain, cassette and chainring life depend a lot on the individual. I clean and lube mine very regularly, don't accelerate very hard, try to shift smoothly, and I got 3000 miles out of my last set. Many people have to replace theirs every 1500. Chainrings tend to last longer, but I think if the LBS were really trying to rip you off, they'd tell you to replace both chainrings. They should be able to show you the wear on the cog teeth. That's easy to see, even for an untrained person (you can look it up online).

I'd be surprised at a derailleur wearing out that quickly. That's what makes me most suspicious. But honestly, if you don't clean and lube it regularly and you do use it a lot, grit can work its way into ANY moving parts and wreck it over time. Again, they should be able to show you the abnormal movement or binding that tells them it needs replacement. That's more a matter of judgment since you yourself might not know what's within normal tolerances and what isn't, but if they hesitate when you ask to see it, that tells you something all by itself.