Not for nothing, but when I think of a pen maker's logo on a pen, I don't want it to "interfere" with the pen. Consider a custom clip with the logo on it? A custom finial with the logo? Center band? Are you using kits or are the pens "from scratch?"
Though I have no experience in this, acrylic would be a great material if you buy an engraving machine. I'm not sure what you're making, so I am a little in the dark...but some fine things in this world are set apart by their very shape. Does it need a logo at all? (We all like to "see our name in lights," but - thinking outside the box - maybe your pen design already stand for something, and you don't need "something else" to let people know "who made that pen." I don't need to read "Coke" to recognize the twisted glass bottle shape.)
Think less about the barrels you turn and more about the other components and characteristics of your product as a sign of the maker.
Attached are pics of pens I have made with a logo using a decal. I referenced the library document as well as a few others I found by searching how to make your own own and apply decals to pens.