I think what will happen will be like thus:
With Action cards that affect cards in your hand when played, it does not matter which individual one of them you trash; they are all the same card, really. With this in mind, having your hand convert into 'piles' of collections of cards that you can select en mass when trashing/affecting seems to be the best option.
When I want to target specific cards for Scheme/trashing (for example), at the end of the turn or during a turn (for trashing), it will show me each card played (for Scheme, trashing would simply show your hand or whatever is the appropriate target) and how many of them there are with a small number, similar to piles. When you select a card, it will move upwards to the top of the screen, away from the piles. If you clicked it again from the top, it would go back to where it was. The interface should also say how many Scheme/trashing choices you have left. After you're done selecting the options, you click on 'Trash' or 'Topdeck' or something of the sort. It is complicated to explain, but it is very intuitive. The only downside is that it is a bit slower, but it does prevent misclicks for sure.