I scan the phone with Malwarebytes no issues.
I do have a ledger but not I don't have coins to put on it .
I totally understand your point since the fund was safe for over 3 years of being dormant. If you are sure that you didn't browse any malicious website before the hacking event then Coinomi system has some bug on there update which we can't verify since they are not an open source code. The best thing to do is to gather all the complainants in different forum and social media outlet to raise concern to Coinomi, The way they are using there Company as answer to your complaint is a bit shady for me. They should give you a technical investigation report to prove that there system has no bug for a potential leak of data.
This is what I try to do...just tell what happen to me.
To open a wallet a PIN is needed , before sending a transaction there is a password that need to be input, the hacker somehow bypass all those..I conclude that the wallet sent the seed out to those who make the upgrade.