Have you created additional identities and enabled Bcc-to-yourself for them?
If not, and the option I mentioned earlier is disabled in Aquamail, then the fact that you get your sent messages in your Inbox is not due to Aquamail.
You should check with Zoho support.
Zoho is rather weird.
E.g. this page of Zoho user guide says: "When a message is sent through the Zoho SMTP server, the server places the sent message in your Sent folder."
But according to that, it should be in Sent folder (which is not reachable via POP connection, only via IMAP), and not in your Inbox. So, check with Zoho.
Are you sure that you access your account from both Aquamail and Thunderbird using POP (as opposed to IMAP) connection? As far as I know, with Zoho, unless you specifically told Aquamail to use POP, Aquamail would create an IMAP account.
In that case, - if you somehow managed to map Aquamail's "Sent" folder to Inbox, Aquamail will save a copy of the sent message to Inbox.
Based on the information you've provided this would be the only scenario that could explain your observations.
To disable saving sent messages in Aquamail (which cannot work for POP accounts):
Long-press on the account -> "Options and folders" -> "Composing and sending" -> "Save sent messages" - uncheck.
