They are as loud as a normal case, althought you tend to notice them more because they normally sit on the desk rather than below it. Vista SPCR and pick silent components. The inbuilt case fan and PSU fan are pretty quite under normal conditions. The machine in my sig is good up to about 35c ambient and then the case fan has to come off its lowest setting. Your choice of GPU will be the biggest factor with noise and then harddisk.
I wouldn't worry about an e series CPU, just get a normal 95w one. The idle isn't that much different (2-3w) and if you want you can easily undervolt it. The PSUs in shuttles are pretty good, I've setup some surprising rigs on their 250w units (overclocked C2D 3.2ghz, 8800gt, 2xHD, 1xDVD). Also I prefer the G case of the P case.
As for working in the case, I much prefer it to a normal case. They are just well designed. The whole drive bay is removeable which basically leaves you working in a metal cage with most of the cables are already routed for you. I'd much rather work in a shuttle than a P180 and I've done several of both.
SZ87R6/i5 4560 stock/24GB 2333mhz/840 Evo 250GB/Seagate 2TB/ASUS 760GTX/Dell 2711
Rainbows lie in corded knots
While thunder wakes the sleeping crocs.