As an automated deployment step, I have a little less of an issue with it, but it's still highly dependent on the client. If they are unaware that you are doing this and do not have the ability to access the clean source files then you are depriving them of the ability to update their site. Sure, sure, nobody wants a client messing up their nicely crafted work, but in the case that you two part ways or you (or your shop, if you're not a freelancer) can't do something for one reason or another, then the product you've sold them is verging on defective unless the crippled source deployment was explicitly agreed upon.

When you do work for someone else, in most cases, the client expects (and usually contractually ensures) that they own the work you do – and it's a reasonable expectation that it'll be revisable.

In general, this just comes off as spending way too much time to prevent something that probably won't happen because rarely is your work as good as you think it is (most of us suffer from this =) and if it is good enough to want to copy, given the nature of HTML/CSS/JS, etc., if you go out of your way to obscure things too much (and if it's a trend), the motivated will find a way to undo your obfuscation in a programatic/easy fashion.

But that's just my take – to each their own...