Shatner & Nimoy were singed for every episode in season one. Whitney & Kelly were main characters but were not signed for every episode.
Actually, I think you'll find that Whitney and Kelley were signed to 13-week contracts. They would have received some kind of minimal retainer to stop them taking other work during those 13 weeks, whether they were needed for a ST episode or not. Ideally, the writers were expected to use both characters if they could. That's partly what made it so desirable for the production to ditch Rand (GLW's health worries an additional concern, and presumably why she got written out of "Dagger of the Mind" at an early stage). She was simply too expensive for a character who wasn't getting enough lines in sufficient scripts, and the writers were stymied by her character being paired with the captain so closely and so early.
GLW's "cameo" in "The Conscience of the King" was originally longer, but it was essentially a walk-on to fulfill her contract/throw her a bone. The 14th episode filmed was "The Galileo Seven", which GLW calls her "least favourite episode" ("Dagger of the Mind" being her second worst) because Yeoman Mears was a last-minute name-switch Rand replacement.
Kelley would have had his 13-weeks renewal clause activated, but GLW was "let go".