Hi Dan,
Actually as far as I know the only thing that uses /App_Data is NeatUpload. We no longer use NeatUpload but it was included in version 2.3.8.9 and it needs it to exist and be writable so go ahead and create it empty and make it writable along with data.
If you upload a file using one of the features like image gallery or from the editor and you see a progress bar then it is using NeatUpload. If you don't see a progress bar then it means NeatUpload is disabled because it is commented out in Web.config. NeatUpload doesn't work in medium trust hosting so it should be commented out/disabled in that case and the folder is then not needed.
In the latest version of mojoPortal we have a newer file upload and no longer use NeatUpload so that folder is no longer needed except if using the SQL CE package of mojoPortal which keeps the database file there.
If you are deploying a new site to Arvixe why are you using an old version of mojoPortal? I recommend always use the latest version for a new site and don't be afraid of upgrading existing sites either.
Hope that helps,
Joe