The current theory (no evidence, since SpaceX is somewhat close mouthed on this topic) is that they are demonstrating that they can catch one, first. Once they understand the process, they will figure out how to do both.
In fact there have been comments from Musk that only one half is even instrumented to be recovered right now.
Boats are well understood technology, and basically off the shelf. The modifications so far are not major, though they look mighty cool!
Solving this by getting a second boat is the simplest solution.
Some people have suggested they might trying to fly the second half into the wind, or in some way delay its landing to give the ship enough time to load a second net and lower the first. Perhaps they will try that, but first they have to understand if they can catch a fairing, and see how well their plan for lowering/stowing it works.
SpaceX has been very good at iterating, start with one idea (Land the Falcon 1 and then 9 via parachute. Grid fins - ran out of hydraulic fluid initially, added more, moved from Al to Ti), test it, see its issues, ditch it and move on to plan B. Then Plan C. Until they finally get it to work.