I have a specific Discover card that I would like to use to book a pair of train tickets (there and back) and a five night stay at a hotel. I would like to book these things online.

However, the credit card I use may have been deactivated—which means it can be used to make online purchases, but not in-real-life ones. The point is that by the time I am at the train station or hotel and have to present to the clerk the credit card I used online, this card may be either deactivated or cancelled altogether.

Will I still be able to board that train and use that hotel room, if the transaction did go through in the first place, online, even though the card's deactive/cancelled?
If you have the e-tickets for the train and a confirmation number from the hotel then the transactions have gone through. You won't have any problems with the train, but the hotel will ask for your card in case you charge anything to your room, or in case you damage the room. Some hotels will accept a cash deposit in lieu of a card; others will tag your room as being a non-service room, meaning you can't order room service or use the mini-bar. Without a credit card on file most hotels will not activate your phone. Of course, if it's a really cheap hotel, they might not care, especially if they don't offer room service.
You expect the hotel and train station to trust you……..how do you intend to pay for the services………in the hotel you will have to present a active card to check in…….