Based on that, they make the assumption the Americans are going to come out and fight them immediately.
Why make that assumption and what do you mean by immediately. Part of the underlying logic of Midway is the USN has to be lured out to fight, because it is the inferior navy. And there is nothing in IJN intelligence that suggests otherwise. You have BDA of Pearl Harbour. You have AAR from Coral Sea, you have Janes you probably have belated intel from the East coast and Panama. The argument is that unless there is a vital US interest at stake the USN would not risk a battle with a superior fleet, and the IJN believes with confidence that the 4 carriers of KB vastly outnumber the carriers the USN has available.
For that to be valid you have to actually credible threaten Midway and even if you know they know you don't know Yorktown will be at sea ( the USN does not actually know either until very late in the day) and don't know how the USN handles its air groups so you don't know these will be full. The working assumption on the available intelligence is the US only has 2 carriers and possibly with reduced air groups.
A flotilla of old slow and expendable ships is not a credible threat. Its target practice for the Midway airgroup which can continually be reinforced from Pearl. Midway can scout 1000 nm from its base and Midway only needs to focus on a fairy narrow sector, the rest can largely be covered by aircraft from Pearl. A fleet moving at 15kts is in scouting range for 66 hours. In fact it was detected at just over 500 m. If its not detected its no threat, when it is while the USN might sortie they will also converge subs on the area and might sink the transports. If it does it ceases to be a threat.
Its really only when the USN has confirmation that Midway is under attack from carrier aircraft or that KB is present ( about 0530 on 4 June) that the threat is material at which point OTL see Shattered Sword. And a strike from a small carrier or even a couple is unlikely to be effective. In order to launch that attack you have to be well within scouting range of Midway.
The USN objective after all is to do damage to the IJN not specifically to the IJN carrier force. If the KB is far enough away to avoid detection, its also too far away to intervene and the US carriers may after sinking the decoy or invasion force decide jobs a good un and retire on Pearl, leaving you to explain why Ichiki and his Butai are being digested by sharks.
Assuming the USN will pre position itself at a location convenient for your carriers to ambush it and stay there means a completely different set of assumptions about the USN strength and the assumption that the USN will close on Midway prior to Midway actually being under threat.
In terms of the effect, probably very little. The US strategic debate is already about Rabaul or the Solomons in fact Rabaul is a non starter for a year or more as the troops are not available. The US has one division available 1st Marines in essence. The other ground forces are the Australians who are not about to participate in Macs fantasies and King is not about to give up his Marines even if Mac begs nicely and grovels. he can read a map Guadalcanal supported from Espiritu Santo is a much better option that defending Espiritu Santo supported from anywhere. Not that the Japanese can do anything, until very late in 42 the IJA can only provide 2 regiments for the whole of the Pacific. One is currently walking up the Kokoda track and eyeing up Hiro for lunch and the other is either shark food or wishing Hiro had been posted there.