Absolutely, I should re-emphasize that the more specific info I posted above was from my personal setup, keyboard, habits, hand-size, and experiences.
Every aspect of your personal situation will make this a very personal experience. Maybe you play guitar or piano so you're comfortable or even used to making some hand shapes other people would be pained to produce. Maybe you have an ergonomic keyboard, or a 14 button mouse, or a gamepad, or maybe you play on a joystick. =)
And, to Irat, well said Kaze! We have an advantage that many of the controllers (keyboard, mouse, etc) are already ergonomically designed. That said, looking at how you design your keybinds can make life easier. It's all well and good to use modifiers a lot, I do, but I found early on that control+Q (ScS/Oblit), control+F (DS), and control+E (deathgrip) were starting to hurt my pinky because of how I was pressing the control key (namely with the outside edge of the finger instead of with the pad). I had nasty muscle cramps and some pain for a while, so I had to fix my muscle habits so I didn't do that to myself any more (pain is a useful tool for adjusting these muscle memory habits, not that I'd recommend including that voluntarily...).
Just because it has become muscle memory does not mean it is good for you, as with Kaze's example of people having horrible posture (speaking of which, depressing to me that Chrysler seems to have takent to designing cars that support people's bad posture and are uncomfortable to sit in if you have good posture) out of habit. You may also get warnings, like I did, of less ideal habits, though some may just be subtle enough that it takes a good long time to become aware of. How many people here rest their wrists on a desk or hard surface while they're typing on their keyboard? Carpal tunnel inflamation waiting to happen there. Add for further complication those readers who are still teens or early 20s. At that age your body is at its most resilient so it could be dealing with minor fatigue more rapidly than you can really become aware of it, but as you get older you will start to find your bad habits start hurting or actually becoming the root of debillitating conditions.