A customer walked in and deposited $14,000 cash. His wife (who was not with him) is a joint owner on the account. Do we include her on Form 4789 under the guise of "multiple persons" (question 1), even though she wasn't present when the deposit was made?

Yup.

If it is a joint account, all owners of the account benefit from the deposit. Therefore, list all owners as beneficiaries. If it is a withdrawal, not all owners may benefit. Therefore, list only those present.

List the owner making the deposit on the face of the 4789, in Section A Part I. In that way, you can check the box for "conducted on own behalf" at the start of Section B, and omit the rest of Section B.

List the other joint owner(s) in Section A entries on the reverse of the form. Check "multiple persons" in item 1 on the front.

A similair issue occurred yesterday. Husband and wife, both joint owners of the account independently deposited amounts that totalled over $10k. After reading the form instructions, which don't mention joint owners, we also concluded it was reportable and listed both names.

You are correct in noting that the instructions with Form 4789 do not discuss joint owners. The reference is oblique, in that we are required to list all persons "on whose behalf" the deposit is made. I think it's a pretty easy segué to assume that, if I deposit $15,000 cash to the joint account I hold with my wife, she benefits.