If it's not something you want to redistribute (eg via a plugin you're building) then adding your own functions / stored procedures is ok. As long as you don't change the Moodle tables structure.
I have several stored procedures that push Moodle student data to QlikView dashboards and XML views that BizTalk exposes to a business consumer system.
The important thing is: READ ONLY. Don't allow any custom functions etc. to WRITE/UPDATE/DELETE data in the Moodle database. CRUD events should be done via the Moodle API's, not directly in the database. Else you WILL break things!
And be sure to check indexes and execution plans, etc. before you change anything in your Moodle database.