I agree that this is a problem, but it applies not only to startups but every proprietary service. The only way, that I can see, to eliminate the risk of losing a given service is to make a personal archive of everything (for primarily data-based services), and only use free/libre software (for computing services). Without the ability to run the service on your own machines, modify, and redistribute; I don't think you can have any hope of long-term availability.

This doesn't strike me as a problem. Large companies also shut down initiatives and projects, and everyone knows that startups are inherently risky, because they don't have a business model yet.