Which wallet software did show zero balance? Was it properly synced and has this been verified (see also next question)?
We all know that Ledger Live is a real piece of shit software that sometimes has some real bad sync issues.
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OP Either you exposed your recovery seed online at some point on a computer with malware, or someone had access to your backup, a passphrase would mitigate this attack if that's the case.
Have you spread your recovery seed backup elsewhere? Someone could have physically accessed it and you never knew! That's why using passphrases is important, but I think this case may be a bit unlikely.