This is just simply not comparable to revealing the same Moat multiple times, or letting you trash cards that give no benefits, or letting you play cards in a stupid order etc. Most of these are judgment calls, and from a software viewpoint, would entail adding more functionality to check which options would be good or bad for you. Let's take Forging two Colonies as an example. There are absolutely instances when you want to Forge cards into nothing. We can't expect the software to judge when you shouldn't. And in any case Forging two Colonies does something. It makes a difference in the game.
The reasons for being able to react multiple times are known. In theory isotropic could check whether there could conceivably be any reasons to keep revealing the same reaction, and of not, not offer it. I would say that would actually make the interface better. But first of all, it would mean adding more functionality, which we have no reason to expect, and secondly, it would give the player hints when the option to react does show up. (I think that last part would be a small sacrifice to make in order to make the interface smoother, but I could certainly see other valid viewpoints.)
Choosing a card you can't top deck, on the other hand, does nothing -- not compared to clicking "none". As Donald has confirmed, the reason for the card text is clarity. Not that there might be a case where you would choose a card you can't top-deck. The isotropic software already knows which cards Scheme won't work on (it conveniently marks them "new"), so it shouldn't present them as options distinct from "none".
The very idea that some of you say it should light up with the read ?!, kind of says I'm right. I can't think of any other examples where I would want that introduced, including Forging two Colonies, or playing Banks before Coppers. I'm guessing you all agree on that.
But I concede that in the event there will be introduced cards which you don't know whether you'll discard until later in the clean-up face, this might be necessary. But judging from Donald's reply, this seems very unlikely. And in any event I'm betting that Dougz has had to go back and change the behavior of old cards before when other cards were introduced.