There are no disadvantages to this command – the RCLSTG and IPL are tasks which you should occasionally run to maintain your system (think of it like a defrag in windows).
The only thing that you may need to check is that all your processes are started again after the IPL. For example if you have an FTP server running on your machine, this may not be automatically started after you IPL. This will depend on how your system is set up – normally if you need certain processes to be started after an IPL you would change the QSTRUP program to start these processes for you. You can find the name of your QSTRUP program insystem value QSTRUPPGM. This is a CL program and you can normally retrieve the source using RTVCLSRC.
You mention deleting a user profile., DLTUSRPRF is the command. if the profile owns objects you will get an error. In that case you will have to transfer ownership of the objects first to another user profile then delete the one that you want to delete.
also you mention CPF9033. here is some info on that:
The RTVDSKINF command receives message CPF9033 F/QODFIND TQEZRCLM.
Message CPF9033 is issued when the RTVDSKINF command finds a noname object stored in a folder, requests the name from program QODFIND, and it cannot find the object in the index. Recovery is to run the RCLDLO command.
If receiving multiple CPF9033 messages, the objects might not be in a library. Therefore, the RCLSTG command should be run first followed by the RCLDLO command. The RTVDSKINF will complete but might wrap the message queue in the process of issuing the message CPF9033.
Previously, this message caused the damage bit to be turned on for QDOC, and the users could not access their folders until the RCLDLO was run. Now this is a warning message, and the documents can still be accessed.