Messages without body-tag are currently not saved in the archive.
However chatmarkers (XEP-333) should be saved, because if a client requests messages from the archive without or a cleared local history, the user can currently not see whether his messages were delivered / read / ... by the opponent or not..

XEP-0313 allows it:

6.1.1 User Archives

A user archive is anticipated to provide the user with the ability to access their prior conversations. To this end, a server SHOULD include in a user archive all of the messages a user sends or receives of type 'normal' or 'chat' that contain a element. A server SHOULD also include messages of type 'groupchat' that have a , but where such history is accessible through another method (e.g. through an archive on the MUC JID), a server MAY exclude these from the archive.
A server MAY include additional non-conversation messages.
A server MAY include messages of type 'headline', but this is not generally suggested.

At a minimum, the server MUST store the elements of a stanza. It is suggested that other elements that are used in a given deployment to supplement conversations (e.g. XHTML-IM payloads) are also stored.
Other elements MAY be stored.