I think it depends on what exactly you're making -- I've made quite a few things by hand: windshirt, sleeping quilt, jackets, bivy, hammocks, tree-straps for my hammocks, backpacking stuff-pillows, stuff-sacks, even one of my tarps. I like to quilt, and do most of that by hand, so making gear by hand was a natural extension for me. Also, I like to sew while I do something else, like watch TV. I made the quilt I did by hand while I was living abroad in Germany, where I didn't have a sewing machine, so that is indeed also a benefit of hand-sewing.
I think the only time you will see a real functional difference between a hand-sewn and a machine-sewn piece of gear (assuming good skill at sewing by hand) is with pieces that are really load bearing, such as backpacks. I wouldn't do one of these by hand, simply because there are several places I'd probably want to reinforce with several lines of bar-tacking, and while this is possible to do by hand it's pretty frikkin annoying! I have made tree straps for my hammock that are perfectly servicable and safe by hand, but sewing those lines through thick webbing several times over is a pain.
I didn't notice any problems at all with down-proofness on the quilt I made by hand, but I was pretty careful to keep my stitches even and small and to do french seams to close up the baffles where I added the down. I use my hand-sewn windshirt almost every day -- have had it for three years now with no issues. Stuff sacks, pillows, etc. are also all still in service -- the hand-sewn tarp I have doesn't get a ton of use, but it's still kicking too! I worry about the reinforcements on the corner, but I think that's all in my head.
Good luck, I think sewing gear by hand is a blast and I hope it works out well for you.