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Does anyone know where the name came from? I assume that the thousand part refers to a chapter having 1000 marines but The Thousand Sons were a Legion right, divided into several chapters of 1000 each.
I was wondering if they were named before the concept of legions existed and their name was never updated.

The Thousand Sons were never broken down from Legion size due to fleeing into the EofT, so they have never been a chapter.

The name comes from the fact that there were 1000 of them and they were sons of Magnus the Red, IIRC.

I realise they weren't broken down, I just thought that all the legions were at least several thousand strong. If there were only 1000 of them then that answers the question thanks.

Several of the Legions had 'lab accidents'. The Thousand Sons were one of them, and the Emperor's Children were another. Some of the last legions were also reported to be small (like the Salamanders).

Also realize that it appears the Legions took a name after their Primarch was located (or even changed names, the Death Guard were the Dusk Raiders before Mortarion was found). So, they weren't always known as the Thousand Sons, probably only after Magnus was found.

It's not clear how many marines were in a typical Legion, but it's known that it varied greatly. Some were around 1,000-2,000 strong, the Sons of Horus were probably over 100,000, and the Ultramarines were somewhere around 300,000-400,000 marines.