Another consideration for where to store the XML (file vs table) is how you will be retrieving the data. Not knowing the specifics of your application, I can only say generically that if you can provide an index to your data, a database will scale much, much better than files.

Final idea -- if you are very worried about execution time of the XML parser, perhaps you could store the result (in a Data::Dumper style hash, say) of an XML parse, rather than the raw XML itself.