I'm pretty sure that Israel, or whoever you want to suspect, would have the ability to covertly attack a non military port without the use of an easily tracked missile launch or drones.
A small remote detonated bomb would have been enough to trigger the explosion on what was not exactly a top secret storage of volatile materials.
Why complicate things with missiles etc if there is an easier and anonymous way to do it ?
It was an accident, but CT need to make something out of it so it's either missiles or aliens.
Assumption that if Israel was involved they had any intention of being covert or that the explosion was the intended outcome.
When it comes to destroying hostile weapon supplies Israel tends to be quite brazen - they'd probably use a missile and stick the onboard camera footage online. There is a small chance here, if there was any Israeli involvement, that the intended target was Iranian ammunition in transit and the explosion was an unintended consequence - but usually their intel is good enough something like that would have been picked up on before the operation went ahead.
I'm not at all claiming Israel was involved or behind this - but I think it would be a little naive to absolutely rule out any involvement - it won't be the first time they've carried out interdiction activity in this manner and had significant intel gathering actively going on over Beirut in the 24-48 hours before the explosion (likely monitoring certain political ongoings).