I bet the publish service, that targets cards, will allow deleting photos from the card that have been deleted from LR.
Photos generally should be deleted from card after imported and backed up - having to put card back in camera to do it is an unnecessary bother.
FAT32 supports long filenames only via VFAT, so its up to the camera manufacturer if they support VFAT names or not. 8+3 filenames should work anyway.
What you probably should read is the DCF specification which specifies how the filesystem DCIM tree is created, see http://en.wikipedia.org/wiki/Design_rule_for_Camera_File_system for specification links.
I guess you are targetting a photoframe using SD cards, not actually publishing to back to camera...?
Seems like the "standard" is more for naming and keeps everything within 8.3 so actual low-level format is mfr choice. Although I still wonder if any serious camera is using a format that does not support long filenames, I think I'm covered anyway - my publish service will stay within 8.3 if necessary.
The publish service is general purpose but has some special options for publishing back to camera cards as an extra backup when traveling.
It's not uncommon for people to bring more cards with them than they will fill, so allowing the extra space to hold backups of some or all of the keepers provides some cheap insurance in case of travel incident. Publish services are ideal for this task, since there's built-in synchronization logic to delete non-keepers, and keep from re-publishing if nothing significant has changed.
As long as it doesn't interfere with the proper functioning of the card, it will be a welcome feature for those who like to travel as light as possible whilst maximizing the odds they return home with their photos.