I used to work for Homer.
The reason penny deals exist, is because the inventory system errors out if you try to make something have a "0.00" value. It's possible it's for tax reasons (well, it's in the store, it's gotta have SOME value!), but that's not how it was explained to me.
The store has already gotten credit for the item from either corporate, or from the MFG/distributor. They're supposed to actually throw that stuff down the compactor. I've got a really fond memory of throwing a perfectly good $800 patio set down the chute. When asked why I can't just pay for it and take it home, the ASM said "Because the store's already gotten credit for it, and we can't do that."
Finding and buying penny deals doesn't hurt Homer at all. You're actually doing them a favor, because this stuff was going to be destroyed anyway (or sent back to MFG). If it's still on the shelves, someone along the line already messed up and didn't do their job.
Penny on. I didn't realize this was a thing that people did until I found these threads tonight. It never occurred to me that items were "missed" when they pennied out.
Another frugal tip: Sign up for the credit card if they're offering free items (usually it's like a stud finder or something else under $50). Takes 5 minutes to approve you, and it does hit your credit report for a hard inquiry (But doesn't actually reduce your score unless you're denied). Take the free item, go home, and cancel the account. I got a lot of free stuff when i worked there using that technique. I probably cancelled 10 or 15 home depot cards.