1. By "OS X Update" do you mean "10.x" update? Or do you mean "10.x.x" update? There's a huge difference between a whole new OS X version and a point release update to a pre-existing version. If you're talking about the the former, then yes, even a well-researched build can sometimes lose compatibility between updates. It's a bummer, but it by no means is terminal nor does that lessen the value of the investment you made initially. Yes, Macs hold their value well and often better than a home-built PC. Though you really do pay more out of the gate, so I'd say it's proportionate. If you're talking about point releases breaking your system, then no, you are doing something wrong, or you researched something wrong, because with Snow Leopard and newer, that really became as simple as "install update, re-apply patches, fix permissions, reboot, done".
2. For a dual-core machine, $600 is steep. For a quad-core machine with no discrete graphics, $800 is steep. Sure, you can resell it in a year or two and have only lost $200, but who wants to buy a machine to sell in two years? If you keep a Mac mini for longer than three years, its value becomes moot. At that point, I'd rather just find stuff that I know has worked for multiple major versions of OS X (so a board that has been known to work with Lion and Mountain Lion), and buy CPUs.
3. The freakin' thing is a desktop, why is WiFi at all important given that Gigabit Ethernet is substantially faster and much more sensible anyway? Bluetooth, I'd understand, though both are moot points given that it takes an hour to research and buy a compatible Wi-Fi/Bluetooth card and maybe another hour to do what is necessary to install it. Really non-issues here.