From the perspective of Admiral Yamamoto, the true goal of Operation MI was not the seizure of Midway Island. While its capture would help push out Japan's defense perimeter even further, the main goal of Operation MI was always the destruction of the American fleet, including not only the American carriers, but also any battleships that had survived Pearl Harbor or been returned to service since December 1941. Yamamoto's design was that this would serve as the grand Decisive Battle that would break American will to prosecute the war, and enable Japan to negotiate a peace from a position of strength.

To that end, Yamamoto approached planning for Operation MI from the assumption that the US Navy was a battered, demoralised organisation, and that it would have to be enticed into leavings its anchorage at Pearl Harbor so that it could be destroyed in battle. To that end, much of the overly complex planning around Operation MI was designed to try and deceive the United States into thinking that the attack on Midway represented a portion of the Japanese fleet that could be isolated and destroyed. To that end, rather than concentrating his force, the Japanese naval units committed to MI were scattered across the Pacific. While Nagumo advanced with the four carriers of Kidō Butai on Midway Island, Yamamoto himself was following a few hundred miles behind with the battleships of his Main Body, including the brand new Yamato. Off to the south, came the "Midway Invasion Force", including the landing force under Admiral Tanaka, a close support group of four heavy cruisers under Admiral Kurita, and the Invasion Force's main body under Admiral Kondō, including two battleships and a light carrier.

Kondō's group (and the rest of the invasion force for that matter) was essentially bait, a force large enough to be worth sortieing the fleet to destroy, but also small enough that--from Yamamoto's point of view--the dispirited Americans would think it an isolated and easily destroyed Japanese fleet. By deploying ships in isolated squadrons, Yamamoto hoped to conceal the size of his force committed, so that the Americans would be unaware of just what they were facing until it was too late. In the ideal world where everything went according to plan, the Americans would sail north to destroy Kondō's force, only to be lured into the awaiting guns of Yamamoto's Main Body and the aircraft of Kidō Butai. Battle would be joined, the Japanese emerge victorious, and the Americans would sue for peace.

So, to answer the core of your question: yes, the Japanese did consider the possibility that the Americans would refuse to attack a clearly numerically superior force, and so deployed their fleet in such a way to conceal its size, in order to provide tempting targets as bait. Admiral Yamamoto based his planning of Operation MI with the assumption that the American fleet would have to be lured out, and that meant trying to convince it that it did not face a superior force, until it was too late. Of course, this same deployment came back to bite the Japanese as--for all their numerical superiority in ship committed--in the actual battle space where combat was joined, the Japanese were actually outnumbered. None of the other ships in the other fleets could support Kidō Butai, allowing the Americans to attack and destroy the Japanese carrier force.