Firstly, we know that Jiraiya knew that Minato used the Shiki Fuujin on Kurama. We also know that Hiruzen witnessed this event and realized that Shiki Fuujin was being used. So, Hiruzen might have told Jiraiya about that part.
Originally Posted by Kirin Rei
Then, lets say my theory's correct. And lets say Jiraiya knew for a fact that shinigami's can only interact with Yin Chakra. He would, then, also know, for a fact, that using the Shiki Fuujin could only possibly seal Kurama's Yin Chakra. Thus, effectively splitting Kurama's chakra. It would also mean that Jiraiya would know that whatever Minato sealed into Naruto could only be the Yang Chakra portion.
Secondly, if my theory were correct, then choosing Shiki Fuujin would effectively mean splitting Kurama's chakra into Yin & Yang. But, choosing a different solution means not splitting. Thus, Minato would ultimately still have a choice as to whether to split Kurama's chakra or not. But, choosing Shiki Fuujin also means choosing to seal away the Yin half. And, since Shiki Fuujin was Minato's choice, splitting Kurama's chakra was something deliberate and Jiraiya would have deduced that.
Also, Jiraiya believes that Minato doesn't do things without a reason. All of this would explain why Jiraiya speaks with such certainty about these things...if my theory were to be right.
Another question I have is why didn't Minato just seal the full Kyuubi into Naruto? We know for a fact that it is neither physically nor conceptually impossible to seal the full Kyuubi into a "normal" seal since that was how it was sealed in Kushina. So, why go through all the trouble? This is what baffles me. I can only speculate and assume that he did it to make it easier for an infant to survive being made a jinchuuriki.