POSIBLE CASE SCENARIO 1
Goku used this when fighting Pikkon in the other world tournament. I do not remember seeing it used anywhere else. Correct me if I am wrong but I am fairly certain that part of the show was just filler. However, I would assume another reason that Super Saiyan and Kaioken are not used together often is that it is not needed.
Goku v. Android 19 - Goku dominates for a small period of time, then succumbs to the heart virus.
Goku v. Cell - Might have worked here, however it seems that Goku's plan all along was merely to show Gohan Cell's moves and prepare Earth for when he would not be here.
Goku v. Pikkon - Not sure why used here and no where else.
Goku v. Yakon - Not needed, Yakon was an inferior opponent.
Goku v. MSS Vegeta - Might have been able to be used here, however the caveat is that they both had agreed they would fight Buu together AFTER they finished fighting. I.E. Goku would not have wanted to tax his body by using the Kaioken.
Goku v. Fat Buu - Again, it seems Goku wanted others to fight/defeat Buu so that the Earth could be saved when he was gone.
Goku v. Kid Buu - Maybe could have used it here, I do not know if there is a solid reason for why he would not have used it. Postulating a theory though, is part of this post. I would assume that because Goku knew he would have to use a VERY strong attack to defeat Majiin Buu, that maybe he felt conserving some of his energy to start/create such an attack (ultimately turned out to be the Spirit Bomb) would be more important than using the Kaioken attack in combination with SS.
POSIBLE CASE SCENARIO 2
There are two explanations I can give as possible reasons why we never saw it happen.
Out of universe - It'd make power scaling villains and other characters even more absurd than it already was. If Goku were able to utilize the Kaiou-ken alongside the Ssj transformations, Toriyama would need to have villains with strength based on that if he wanted them to still be challenging and intimidating. Likewise, characters like Vegeta would need something thrown their way to make them still relevant when it came to those enemies.
As such, Toriyama probably dropped Kaiou-ken just so that he could keep them scaled a bit better.
In universe - After Freeza, there were only four enemies that Goku ever faced, and only two of those he legitimately wanted to win against: #19, Cell, Fat Buu, and Pure Buu (Cell and Fat Buu being the two he didn't really want to beat on his own). With #19, had he not been under the strain of the heart virus, he would have beaten him perfectly well with his Ssj form, so using Kaiou-ken would have been an unnecessary strain on his body.
With Pure Buu, using something like a 5x Kaiou-ken while a Super Saiya-jin 2 would have been less of a strain than using Super Saiya-jin 3. However, even the normal Kaiou-ken can only be used in brief bursts, which would make fighting someone like Buu (with tremendous stamina and regenerative abilities) very difficult. Even fighting with the sustained intensity of Super Saiya-jin 3, Goku couldn't put a dent in Buu's stamina, and I don't think that Super Saiya-jin 2 with a high form of Kaiou-ken would be able to keep that pressure up.
The Kaiou-ken's not suited for sustained fights. It's best for situations where it can blitz an enemy (preferably one without regenerative abilities) with overwhelming strength and speed
