I don't own a compact (yet) but from a mechanical standpoint, you normally see equal or better accuracy out of short-barreled pistols because there is less barrel flex. For example, G26/27 pistols can turn in some really outstanding groups.
However, the practical accuracy of the compact is going to be affected by the shorter sight radius. How much it will impact things is dependent on the shooter's skill.
Also, there is probably enough variation in tolerances from gun to gun that any given compact is more accurate than a particular full-size model, and vice-versa.