From: Olympia, WA
ORIGINAL: USS America
Yes, it does affect air groups, LCU's, and at least the Allied ship arrival dates. Not sure about the Japanese ship building effects.
The way you can tell when things will arrive is the same as usual, by looking at the arrival lists. When the game is started, every arrival date for each unit/group/ship is randomized by the +/- 60 days and then put on the arrival list with it's new date.
It can be nice, particularly for the smaller scenarios, when players become very familiar with their opponent's arrival dates, but it has one major drawback. Many capital ships normally arrive with escorts at or very near the same time. With everything scrambled, you might have to wait months for escorts to arrive for your capital ships, etc.
I originally played with Variable reinforcements on (either +/- 30 days or 60 days), but have switched to historical reinforcements for just the reason you posted.
It helps to have an honorable opponent who doesn't camp out near the entry points to nail your new ships.