They didn't want Nick Locarno in "The First Duty" because using him as a main character on VOY would mean Paramount would have to pay "The First Duty" writers every time they used the Locarno character. They didn't want to do that so they created Tom Paris for Robert Duncan to play.
I thought Paramount owned the intellectual property; they bought it from the writer for cash up front.
Did Carey Wilber ("Space Seed") get royalties for THE WRATH OF KHAN? I don't think he did. Paramount owns the characters, the music, the whole deal.
I think it varies from writer to writer and what contract is signed at the time. Harlan Ellison, for example, sued both CBS and Paramount for the use of elements from the TOS classic "City on the Edge of Forever" in various tie-in stuff and a settlement was reached.
"It ain’t about the ‘principle,’ friend, it's about the MONEY! Pay Me!"