For several years the summer ferry schedules to the islands were reasonably predictable (although the official schedules are not published more than a few weeks ahead).
Last year, however, that began to change as the Greek fleet is aging and the current government is not as liberal with subsidies as the previous socialist government.
Another factor is changing ferry use elsewhere such as the Baltic and the UK to France routes.
So in 2005 there was a definite shortage of "economy" or deck seats during the high season. But plentiful first class tickets on the high speed ferries at nearly double the price. From what I have read this trend will continue as more standard ferries age and more high speed are moved to the Aegean from elsewhere.
This may hurt the student backpackers' budgets but most travelers seem to have more money than time, so they will be O.K. in their island hopping.
There are more particulars on our Greece page.