In some cases, yes. I am in the midst of preparing a post on this subject. There are some interesting inconsistencies in how DVDA 2.0 handles VOB files. The preview of this post is that VOB files placed in music compilations are handled differently than when place directly on the main menu of a menu compilation. In particular, in one case the audio is recompressed, and in the other it isn't. I'll provide more details later.
John is right about where you place a vob. VOBs contain more than video and audio. There is navigation data that should in most cases be stripped before using as input material.
The next important question is where did you obtain the vobs?
None of us support violations of copyrights. I have not tested DVDA2 to see
if it strips the information. I suspect that leaving it in can cause audio sync
problems.