You can certainly choose to leave the Identifier field blank if that better serves your local description and arrangement practices.
AtoM is a very permissive system - we've intentionally made it this way because there are many cases where local practice differs from the exact requirements of international and national standards - often for very good reasons! Rather than making the fields that the relevant marks as Mandatory required, we have instead simply added warnings that appear on the view page for authenticated users when these fields are not populated. These warnings are never visible to public users.
In fact, you can open a new blank record template in AtoM and hit save without adding any data at all, and AtoM will let you do it!
A couple considerations as you make these changes:
First, if your permalink settings
are currently set to use the identifier or the reference code options for the slugs created when you save new descriptions, you'll want to reconsider this. Without an identifier to use, AtoM will instead generate a random alphanumeric string to use for the slug. I suggest testing this out with a draft record - remember if you need to manually edit the slug after creating a new record, you can use the Rename module on archival descriptions. See:
Next, if you are using the sidebar treeview, make sure your sort options
(in Admin > Settings > Treeview) are set to manual. The identifier and identifier-title options are buggy and I don't actually recommend that anyone
use them until someone wants to sponsor a fix (it's more complicated than a simple bug fix, unfortunately), but the issue itself stems from the code trying to sort on identifier values, and what happens when it encounters records with no identifier. Essentially, your treeview can get caught in a weird loop showing the same handful of records over and over! If that happens, change the setting to manual, and have your IT team clear the application cache and restart services. If it persists, post a message here and I'll provide further suggestions for resolving it.
Finally, I'm pretty sure that with reference code inheritance, if there is no top-level identifier it will still work, and will just build the reference code without that particular element. However I do suggest you do a quick test and confirm that it works as you need. It works fine in 2.4 and I can't think of anything changed in 2.5 or the upcoming 2.6 release that would alter this, but better to be safe than sorry!
Of course, you could always manually add the accession number as the identifier on your top-level descriptions, but I understand that this may not be desirable - you may want to keep the accession number private for security reasons, and it's more manual work! But just putting it out there as an option, in case the above does not work as you expect.