It does indeed mean that if you put 4Gb RAM in a Core 2 Duo mini it will only be able to see 3Gb of it. There is, however, no real downside or risk in fitting 3Gb RAM into the system even though Apple only specs it up to 2Gb. The only 'issue' is that to fit 3Gb, you would need unmatched RAM modules (1 1Gb and 1 2Gb stick) which means you loose the optimum performance of matches pairs of RAM. However, the loss of performance from that would generally be exceeded by the gain in performance from the additional 1Gb RAM available to MacOS.
Upgrading RAM yourself is not easy, but it is certainly not hard for someone with a little experience of working inside computers and who can do such work with care. You need a couple of thin putty knives (or pastry knives if you are more at home in the kitchen than garden) to get the case open, and some disassembly is required, but it isn't a difficult task. If you look down the page at
http://eshop.macsales.com/shop/memory/mac_mini/intel you'll see links for a video of what's entailed.