One major downside is that it becomes really hard to do transactions, especially across multiple files. If you store mostly immutable data though like git (where except the refs every object is immutable, mutating creates a new object) it can work nicely.
Hmm... is the mutability of data really enough to create a need for transactions?
For example here on HN (which afaik also stores the data in files) you can change a comment you wrote. But that type of mutability does not call for transactions, right?
