Yes and No - it really depends on the modification installed.
Some do automatic template edits which will hopefully NOT work for your mobile style due to the fact that the templates in the mobile style are so different to the default style (and other full featured vBulletin styles).
There are some modifications that need their plugins edited so they don;t affect your mobile style - this is a case by case basis.
It is always best to test on a not live site before implementing on your live site so you can work out if you have any conflicts.
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