It's just English. English doesn't always make sense.
"Oh my god" doesn't necessarily mean that you have a god.
"Thank god" is just an expression of relief.
Who knows, maybe the language of religious people rubbed off on others.
I don't see how English being weird or phrases like "oh my god" or "thank god" relate to saying a prayer before you eat if you don't believe in a higher power. Those are just phrases that people use and they have no indication of you believing in a god. But saying a prayer requires you to believe in a higher power.
That's the whole point of a prayer, communicating with the higher power you believe in. Maybe a moment of silence would be something somebody that doesn't believe in a higher power does before they eat. But that's not the same as saying a prayer.
A moment of silence could be the person reflecting about what they're grateful for in life. Or it could be them just thinking of what went on that day. Or a bunch of other things, none of which require the belief in a higher power.