Well, that's actually a difficult question. I try to avoid direct questions and use a passive instead, if possible. (For instance: Do you really want to close aMule? -> Should aMule really be closed?)
I think the formal form is used more in France than it is used in Germany and I don't believe anyone would feel offended if a program addressed this person using the informal form in German.
Thus, it is ok to use the informal form (I think for Dutch, too), but only if the complete translation uses the informal form. Because you started the translation with the formal form already, I suggest sticking to the formal translation.