I thought the setting perma day only worked in single player. But maybe I'm wrong, I haven't tried it out in multiplayer yet. The only thing I have changed was setting the weather to fast, and I have turned nothing off. So the only difference in my client is a slight fps boost (although some might say that is cheating as well, not too sure myself).
Anyways, I'll respect the decision of the staff and find another server for now. I mostly use Spout for saving favorite servers, so even if I don't play Spout servers, the option of having a favorite servers list is too good for me to give up, no matter how good this server may be. But I heard that Notch is planning on adding a server list feature soon, so if I can save favorite servers without Spout, then I will give it up at that point and reapply.
Edit: I just did some tests, and the permaday doesn't work in multiplayer. I tried no rain, but it made my client crash so I couldn't test it. As for clear water, I didn't really see any difference in either single player or multiplayer, so still not sure if clear water works in mp or not. Someone told me that the only things it does by itself in multiplayer are give a slight fps boost and slightly change the interface though.