While the reason for not having a command console might not be entirely due to Steamworks, I do think it makes it a much harder decision whether or not to put it in and alters just what the command console actually does for devs. I mean, if Skyrim is a Steamworks game and it has the Steam achievements. Then they're surely not going to allow the same open console that previous Elder Scroll games have had? Basically you could just openly cheat to get the achievements pretty much instantly (something of which I couldn't give a rats *** about personally, but people like these achievement things.)
This Steam thing DOES effect in-game consoles and editors.
Civilization V has no ingame on-the-fly World Editor like Civ4 had, which has completely ruined it for me. They did release a separate game builder through Steam, but its simply crap.
Also Total War Shogun 2 doesn't have a command console, which all previous TW games did. Shogun 2 is the first to use Steamworks.
With previous Elder Scrolls games, the command console has been completely open and free. From item spawning, stat altering, experience gaining, quest warping etc. These things influence my playtime in game. Its one of the reasons I spend so much time playing them along side player mods. I dont want this to change due to some stupid bloody security thing. It will seriously spoil the longevity of the game for me.