I can understand why Riot may feel it wants an NDA. For example, the Skype chat may be a place they want to be able to casually talk about things that they want to keep private (such as discussion about the methods they use to detect hackers). And they'd want to have comfort knowing there's an NDA they can rely on to prevent the chat leaking. Having been a Wrench for Riot (volunteer tech support role) I can also say I have personally never experienced anyone at Riot trying to influence me or telling me to do something I would not have done myself.

That being said however, the subreddit mods have control over what is the primary method through which people view LoL content and are therefore extremely influential. The biggest concern is that there's the potential for a conflict of interest here. Even if Riot isn't explicitly exerting any influence on the /r/leagueoflegends mods, there's still the risk that the moderators may feel pressured when making decisions such as content removal. Even if Riot never actually asks for it. Or if anyone on the moderation team takes an action, there's the risk it's interpreted as following orders from Riot, even if it's not. That's also ignoring the issue of how this violates the Reddit user agreement.

I think the best course of action would probably be for both sides (Riot + Moderators) to come up with a public policy about how they intend to interact and engage with each other. This would give the people on the subreddit, the content producers whose work appears on the subreddit, and others comfort that there's never going to be any conflict of interest or undue influence.