I am not a Slip collector either. However, Target likely pays extra to be able to advertise and sell the exclusive edition with special slip and sometimes, extra content, etc. By throwing them out, they're killing most of the 'exclusive' marketing promo, important to the 'collector' niche.
I think there are plenty of average customers who happen to stumble into Target and pick up movies on 'new release Tuesday' while they are there-they get home and may ditch the slip, themselves. For them, they don't care about slipcovers, and whether the movie has it, or not, since they are paying for the movie itself and are not comparing editions at different stores. But, if I was a slip collector, I'd be livid-the same way I'd be livid, if I saw a Steelbook looking like it's been through a nuclear war...