This may seem a fairly basic clarification, but it would greatly change the two-player version of the game depending on how the rules are read.

There are a number of cards with the wording 'if you have more than one opponent, choose an opponent.' and then an effect pertaining to that opponent.

What happens to this effect in the two player game? Is the effect nullified completely because there is only one opponent, or is the opponent chosen by default (being the only other person playing)?

You should virtually always take the card literally at its word:

"IF you have more than one opponent" means that if you DON'T, you CAN'T.

"If you have more than one opponent, choose an opponent...". If you only have one opponent, you don't meet the restriction on the "if," so you don't get to choose anyone in the first place. These effects are completely useless - and can never be initiated because you fail the play restrictions - in a two player game.

Thanks for the clarification. It was the full stop (period) after the choose an opponent sentence that made me wonder.

Note that, while the effects are useless, the cards themselves can still be played in a 2-player-game. CS Varys is a perfectly playable, albeit subpar, character even without the effect. The same with the "Mutual..." plots. Mutual Cause especially has pretty decent stats, and has seen play in tournament-level decks up to last year, at least. You won't see any of the others in competitive decks, but there's no reason those cards couldn't be played in a limited cardpool environment.