> How do you mark something for deletion?

The same as you'd delete anything from any protocol essentially, you delete it locally. If you've shared it on the internet, you ask people nicely to delete it, if they refuse, you either pursue them legally or give up. Basically, just like how you delete a picture from the internet today.

> Seems easy to DDOS by changing one character many times in a file which generates a new id each time

All you're doing in that case is adding more files locally and filling your hard-drive with random files. No content gets automatically distributed unless people request it.