I would expect arbitrage between timeframes to force interest rates to be calculated from the point of the slowest timeframe.
Fundamentally, interest is set by what can be done with some capital - what high yielding investment can be made with it in the allotted time period for the loan. If there's some booming technology which offers returns of 12% (because it's just that awesome) per year, but my factory only offers 3%, why would the banker lend me money at <3% when he could make his loan to someone in the tech field and get <12%?
Similarly, if I'm hopping on a rocket to go mine on Alpha Centauri and time dilation cuts my years in half to just 5 years of work, then why would the banker give me money when he could give it to someone who will stay home and get 10 years of work done? I might be the better deal, but if so, I had better return with some awfully expensive rocks 10 years later.
Of course, this implies that investing and then going on a relativistic cruise is a good idea. But why not? That capital you are investing came from somewhere. Where did it come from? It came from someone working hard and then not consuming. Someone(s) chose to work hard and generate $1 million of value, say, but then chose not to go out and hold an orgy of buying $1 million of chocolate and flatscreen TVs. That $1 million of value remains and presumably circulates and supports further investment and growth, which themselves will compound and compound. When that investor returns centuries later, he deserves whatever is left of his investments.
(Given the past few centuries, I wouldn't place high odds on his investment growing to Bill Gates sizes, or there being anything left at all. So such investors would be doing us an even bigger favor than it seems.)