This may be an issue with other cards as well (I'm thinking Lookout is the other big one here but it came up for me in a game with Jack).
I play a Jack of All Trades, and let's say that before the Jack is played I had one card in my draw pile. I gain my silver and then now I'm looking at the top card of my deck. There's a window which shows me the top card of my deck, but while that window is up, my deck still displays that there is one card in it.
This is misleading, because that card is not on top of my deck, it's in my hand in being-looked-at-land. The display should show the number of cards that's actually on my deck at all times.
I agree. I have once forced unwanted reshuffle because of it.
This is especially true because it has been established that if you trash an Overgrown Estate with Lookout, you draw the next card from your deck, not counting the cards you are just looking at due to Lookout.
With Jack one could argue that the card is still on top of your deck while you look at it, with Lookout this point of view is impossible.
I've gone through all the cards that I can think of that may have this kind of problem, and in version 1.2.10 only one still has it: Pearl Diver.
All the others, when they show you cards from a deck, will not include them in that deck's card counter.
I think it should be changed for Pearl Diver, to make it consistent with the other cards. But since Pearl Diver is AFAIK the only card that looks at something not coming from the top side of the deck, it may not be easy to implement.