I figured this was a no-brainer, but after looking into it a bit, I'm not as sure. The http://www.uesp.net/wiki/Skyrim:High_Resolution_Texture_Pack lists a few bugs, including missing textures on certain objects and water glitches on "certain ATI video drivers". As I have a Radeon card, this sounds worrying. Plus, it says the only way to remove it from your Steam account is to contact customer support...

So what I'm asking is how common exactly are these glitches? Are the missing textures missing for everyone who installs the pack, or is it only for some?

To deactivate it, you simply uncheck it in the launcher. Removing it is if you want the extra 3 GB of space back. However, that's really a minor issue since those 3 GB probably should have shipped with the game.

As for the ATI specific stuff, it isn't. The texture is just that: textures. If there's an issue specific to ATI/AMD solutions, then it's likely a driver issue or something similar.

As for the missing textures and such, there's a third-party fix (2 - 3) on the Nexus you can download and use.

There are two mods that fix a number of problems with the pack - http://skyrim.nexusmods.com/mods/8236 and http://skyrim.nexusmods.com/mods/14719.

As far as I know, the glitches are on specific textures (eg logs in a fire or chopping block) and affect everyone.

Alternatively, there are high res mods like http://skyrim.nexusmods.com/mods/607.

Pretty sure the water flicker issue will happen with or without the texture pack enabled anyway and like Death said above there is a fix on nexus for the few missing textures for the pack.