The question is so full of misconceptions & misinformation that it cannot be answered as it stands.
Mozart was not buried in a pauper's grave. He was buried in a common grave, as was the custom for the time for all except royalty & the aristocracy.
'Common' literally means 'not royalty'. A common grave was therefore a grave for a commoner. It should not ever be confused with a communal grave or pauper's grave.
It was an individual grave for the person interred.
The rules at the time also dictated that common graves would be disinterred* after 10 years - something which did not happen to the graves of aristocrats or royalty; they were supposed to be 'forever'.
The reason there were no or few mourners in attendance was that it wasn't an accepted practise at the time. Mourners did not go to a funeral, they went instead to a memorial service. Many memorial services were held for Mozart, as a man of high esteem. They were well-attended, as befitted his status… but no-one ever kept records of who attended, so whether other masons did or did not will never be known.
One would assume they went, the same as non-brothers.
Refs: Wikipedia: Wolfgang Amadeus Mozart and Mozart and Freemasonry
*For what would happen after disinterment, see Ossuary.
More theories about his death are examined in Death of Wolfgang Amadeus Mozart, though none are conclusive.