There are 2 recycle bins. First Stage and Second Stage. If during a backup there are contents in the recycle bin they will remain there. There are variations in the versions of SMSP as to how this is handled for restores. SMSP 7.x and below will ignore restoring content if it is still located in the Recycle Bin, with SMSP 8.0 you can choose during a restore to ignore if there is content in the Recycle Bin and force restoring to a document library, list, etc.