Well, Sardonyx has four eyes, but once I remembered that since she should have five (Garnet has three, Pearl has two, do the math), so I decided to give my take on why she has four eyes only.
Remember, this is just my opinion, It's not canon or anything. You know the usual, read and review.
(Crystal Temple, Kitchen)
Garnet was cutting some vegetables and putting the remains on a pot. And then Steven arrived.
"Hey, Garnet, if you have three eyes, and Pearl has only two, then why does Sardonyx have four eyes?" Steven asked.
Taking his question into consideration, Garnet stopped what she was doing and scratched her chin.
(During "Cry For Help", Sardonyx's Incomplete Realm)
In an orange void that had several triangles shaped like Sardonyx's hair, Pearl looked around in excitement as Ruby and Sapphire stood far away from the Gem. "Okay, Sapphire, we're fusing with Pearl." Ruby informed before pausing and taking a deep breath. "It's time."
"Time for what?" A worried Sapphire asked.
"I'm going to take primary control of the fusion, while you stay behind and provide passive abilities." Ruby answered.
"But Ruby, this is Pearl we're talking about!" Sapphire remarked with worry. "Are you sure you'll be able to stand being in control of Sardonyx with her?"
"I must do this! I won't let you suffer Pearl's obnoxiousness!" Ruby stated with determination. "I must do this...for you, my love."
Shedding a single tear, Sapphire and Ruby separated and the red Gem went to Pearl. As Ruby and Pearl held hands and the fusion reached it's completion, Sapphire remained at the sideline and wished Ruby good luck as Sardonyx's realm fully materialized and Ruby and Pearl literally got chained in control together.
(Back in reality)
Garnet hummed, shrugged and replied, "I don't know."
The End