Depends the system.
3.5 probably yes since wands of X which can trump most skills are so easy to obtain.
Earlier versions where spell slots are a lot more sacred and I would say no. That in individual instances yes but over the course of a story, no.
Personally I think magic should have greater scope (effectiveness) than mundane skills but with much higher costs, price, risk to offset it. Unfortunately spells slots are not much of a price unless they are very limited (this includes magic items in the equation).
If I had to make a choice though, I would 100% want magic to remain potent.
In terms of thieves, I actually wonder sometimes if a thief should even be considered a normal character class or archetype anymore in a game that has the D&D type meme.
They seem to have had so many issues (magic trumping, initially they lacked combat prowess, then their specific combat abilities were very vulnerable to so many factors).
It seems it as an archetype has somewhat disappeared in 4E even (it is not really a 'rogue' as much as a a well...striker

).
While I love stories with thieves maybe they just don't mix well with stories with magic (at least player controlled potent magic). Though I will say it has never been a problem in games i have been involved in, there are enough accounts where there have been issues that it is obviously something that challenges games.
Controlling the use of magic and having magic remain potent has always been a delicate issue. Pretty much all ways of dealing with it have certain issues and you really have to decide what is most important to your game (a pretty obvious statement I know)