I ordered a 2 for 1 deal. The package arrived but it was ripped & the freebie book was missing. :(  Unfortunately the mailer just mailed in a paper envelope with no tape & the envelope was rather large for just the 2 smaller paperbacks, so it's easy to see how it happened.

I know I still need to mark it as received, but should & how do I kindly let the sender know that I didn't receive the other book & they may want to consider mailing books a little more securely in the future?

Yes, I would just PM and let them know that the book fell out of the package. Sometimes people cannot imagine how that happens, I find it helpful to explain how the package might get tossed around, and as that happens, if the books are loose inside the wrapper, they can rip their way right out of the package. And then I say something like "Most senders find that fastening the wrapper tightly around the books with packing tape helps to prevent this type of problem."

What Sara said.  Because of how rough the mail sorting machines can be, I recommend folding over and taping down any excess packaging, and using packaging tape on all edges, corners, and seams.  It's a kindness to let her know.