Speaking as a runner and downhill skier, I say that babying your knees and conserving energy is over-rated. If the OP enjoys riding in this fashion, then s/he should just keep doing what s/he's doing. As for long term health issues, it can't be any worse than running (probably better, since even pedaling hard lacks the pounding shock of footfalls); that is to say, it's good for you, it'll make you stronger and live longer.

Short term health issues might arise if you don't maintain your drivetrain. Standing out of the saddle, I've broken a chain, a cassette cog, and a pedal. The first two broke as I was cranking from a stop in a tall gear. I was lucky when the cog broke and landed on my feet, and less lucky when the chain broke and landed on my top tube. The pedal shearing off of the crank was the unluckiest of all, as it happened during a hard +25 mph sprint, and I landed on my back, in traffic, with road rash down both flanks, some gorgeous bruising on my shoulder and hip, and a bloody calf from 8 or so neat little chainring tooth shaped holes in my leg. The ring had pierced my Achilles, and I couldn't run for about two weeks. The pedals were Kona Jack *****s, and never was there a more aptly named component.

Like others have said, if you aren't using the gears, you might as well lose 'em; then you can run a nice, sturdy SS chain.