It's not BS. It's simply a decision, you don't have to like it but you're not the one making the game either. Going dual layer or adding another disc will increase the cost of producing the game. Would it really be worth it for a few gags and an extra cutscene? Since we don't know the contents of what was removed and Kojima has shown exceptional foresight in overall polish in his games, I'm inclined to believe it's not worth it. Plus if it means that something that's not completely mindblowing is removed just so I don't have to switch discs in the middle of a game, that's awesome.
MGS3 is so packed with goodies and stuff that I doubt any one player will ever see -everything- in the game. It's also so varied that just about everyone has a different experience with the game using different weapons and tactics and finding different secrets and triggering different optional scenes and stuff. If he didn't say anything was removed, we wouldn't even for a moment wonder. So it's not an excuse, it's just a game design decision.