They changed the way the system runs now. Previously systems used to run using the kernel from the /sapmnt<SID>/exe location (DIR_CT_RUN). Now every component in an instance has a separate exe location (DIR_EXECUTABLE) and they run from that location. If you check the existence of the msg_server file, it should be present only at the /usr/sap/<SID>/ASCS<NN>/exe location. I wouldn't bother much with the space consumed by these files. I believe only the ones that are required by the system will be copied by the sapcpe program. If there are unwanted files in the DIR_EXECUTABLE location I would stop the instance and delete all the files under the DIR_EXECUTABLE location and trigger sapcpe program against the instance profile to have them synchronised.
RB