I'll take the Timothy Dalton economy of humour anyday over stupid cracks like that. Are stupid lines like that be the writer's attempt to make Brosnan "fun" to watch? Also, how about keeping Bond in character? He never gave a damn about Q's feelings..
I think it's a classic example of writing-by-committee: the "joke" is there simply because "the formula" dictates its presence. Wouldn't surprise me if there's an Eon rule stating that in every x minutes of chase/gunfight action there must be at least 2.4 sight gags and 3.0 verbal jokes.
In other words: "This is great stuff, but we can't have Bond's car sliced in half without a quip in response from Bond." "Why not?" "Well, we just can't. Add a quip, please." "But maybe the scene would play better without a joke from Bond? After all, cutting the car in two counts as a sight gag, surely?" "No, put a joke in. Audiences would expect it."
Besides, it's an exceptionally lame line - couldn't they think of anything funnier than "Q's not going to like this"? Doesn't even make sense - after all, Q's not the one whose transport has just been trashed and who may only have seconds to live.