I'll say a blend between riding the winning name, and going with accepted custom.
Glass marble companies did try consciously to compare their marbles to real stone - in what we would now call a fraudulent manner. However, "agate" had become an acceptable name for glass marbles in the 1800's.
I need to confirm the dates but I believe that by the early 1900's, real stone marbles were called "realers" to distinguish them from glass ones.*
In other words, "agate" was a name for toy marbles, whether made of stone or glass or even ceramic. And so it would be natural for someone who sold toy marbles to consider that as a possible choice for their company name.
*edit: and then even the name "realer" was co-opted by Peltier for glass marbles, but that's another story! lol