I'm not so sure I'd agree with pafkata90. I believe in optimising your own work environment. With respect to using a computer your choice of physical hardware, operating system, software and keyboard layout can have a huge impact on the way you work. Therefore do what you can to make it easier.
If your children are lucky enough to dictate their own environments - or rather they have their own computers and are not confined to their school workstations, then I'd say take advantage of it.
Changing keyboard layouts isn't trivial - but it's getting far easier for the more modern of operating systems. Make sure they know how to switch layouts themselves. You can get by on Qwerty even if you do use another layout for the rare times you need it, and those times where your layout isn't available. Qwerty is unavoidable.
I'd have thought that younger people wouldn't struggle to learn duplicitous keyboarding skills. The younger you learn, the easier I'd expect it to be. The biggest challenge I'd have thought would be getting them typing in the first place. You'll need an activity that encourages typing - something fun.
If anything I'd seek some advice on correct touch typing technique, and get them into good habits early on. Including a 'healthy' posture. You could seek out an experienced tutor for this (however they may not grok Colemak!) Learning an alternative layout - will at least encourage them to actually type blindly - that's if you don't change the key caps.
My concern personally would be the lack of a good scientific backing of Colemak itself, making it harder to justify the layout to others. Going by the testimonies on this site though, there appears to be a profound preference to the layout over Qwerty - so there is anecdotal evidence supporting it. Then there is your own belief. If I personally believed that Colemak was vastly better than Qwerty and thought it was a great skill to have - then I'd be happy to pass that skill on to my kids.
Either way children are amazingly adaptable - and are fast learners, so I don't think you haven't much to loose. Learning to touch type later on in life for me was a pain. It was not a pleasurable experience and pain drove me to it. This was partially induced from not touch typing. I really regret not learning the skill earlier.
We had about two computer suites when I was at school - and I personally received about 6 lessons (if you can call them that) on an Archimedes computer using typing software. That hardly made an impression. I wasn't lucky enough to have access to the lab, or a computer at home to practice on. Typing is a nice skill to have, and currently text input seems inescapable in many workplaces. The easier it is to key - the better in my opinion.
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Physicians deafen our ears with the Honorificabilitudinitatibus of their heavenly Panacaea, their sovereign Guiacum.