While there's merit to the "just play 4" argument, it is somewhat outdated deck design (for main decks). A lot of very good deck builders like Sam Black will tell you that running 1s and 2s of different cards isn't really a problem. It's all about the probability of drawing it by the turn you'd want it, and how much it detracts from your main strategy. Even a 1-of card is worth having if it's the only answer you have to a corner case scenario that you cannot win. If you look at a lot of top decks from the last rotation, you'll often find things like 1 of a given utility land, or a mix of 1 and 2 copies of various removal.
Where you're 100% right is in sideboarding strategy. A sideboard full of 2 copies of a bunch of cards that answer specific problems with your deck that aren't addressed in the main board is almost worse than nothing at all, and speaks to flaws in the design itself. You want to pack your sideboard with cards that are either absolutely vital to surviving a given deck (ie. ways to break combos in Modern) or more powerful in a given matchup than your main deck. You want the things you put in to actually be stronger than what you take out, and that's pretty much impossible with pairs of cards shoved into the gaps in your main strategy. Often, the sideboarded deck just ends up weaker anyway, and you're better off not having it. It's part of learning how to sideboard properly.
For black in Theros, I really don't see any reason not to play 4x Thoughtseize all the time simply because it is black's most powerful card and it is a universal answer. There's very little downside, and in the rare situations where the card is a bad matchup (vs. some aggro, for instance), you can make them the first thing you side out for cards that work better vs. your opponent.
