Why would you need a method to get round a max materials index error caused by custom maps if you only run stock maps? So in answer to your question - no, a blank mod.arena is not "intended" for servers which run stock maps, as stock maps arent the problem - its custom maps.
You can use EITHER a blank mod.arena file or one which has the names of the custom maps used on your server as a method to defeat the max materials index error. Both do the job.
However, if you use custom gametypes, then you will need to fill in the mod.arena file, as you need to specify what gametypes a map is compatible with, and that is done via a .ARENA file.
Dont worry about what JD said about including materials files for the ingame map vote system - that bit was intended for modders and mappers. Server admins can ignore that part of his post.