Hi Vjolo,
Ideally I would reinstall the HANA database if lm_structure is missing.
lm_structure should have been there with 46 itself.
Install SPS05 again. Check if lm_structure exists and then apply 52.
What's the role of this system? Sanbox, Dev ,QA or Production?
I can understand if the system is already live for corresponding system role use, it's a pain to redo all this stuff. In that case i would recommend raise SAP message, may be they can take a look your system install integrity.
Let us know how it goes.
Regards,
Srikar