My hypothesis is that bioinformatics favors text files, because open source tools usually start as research code.

That means two things. First, the initial developers are rarely software engineers, and they have limited experience developing software. They use text files, because they are not familiar with the alternatives.

Second, the tools are usually intended to solve research problems. The developers rarely have a good idea what the tools eventually end up doing and what data the files need to store. Text-based formats are a convenient choice, as it's easy extend and change them. By the time anyone understands the problem well enough to write a useful specification, the existing file format may already be popular, and it's difficult to convince people to switch to a new format.