Yes this will be a big problem....
... Once bitcoins hit $100 million each and the minimum buy in is $100 for one satoshi
Until then I'm not worried
You raise a valid point.
The entire world economy is $80 trillion. Let's say Bitcoin replaces the USD entirely, for a net worth of $15.685 trillion (2013). Assuming it doesn't take until 2140 to do so, we'll be working with about 18 million BTC.
With a market cap of 15.685 trillion, each BTC would be worth $871 389. So it's never going to hit $100 million that way.
However, to get that big, Wall Street would obviously be heavily involved and screwing around heartily. The total derivatives market is about $791 trillion. Assuming they can reach even a quarter of that with BTC, and start further inflating the price of BTC to serve as a base for a new fractional reserve currency (don't lynch me) $197.75 trillion. That gives each BTC a value of $10 986 111. A satoshi will then be worth 10 cents.
I'd say we will never have to worry about the indivisibility of a satoshi. Ever.