Like many others, I'll build mercs if I have a buttload of resources, but nothing to spend them on. The ship cap is pretty huge (something like 400 with high ship caps), and since they're so bloody expensive, you're not likely to reach it. If I do build them, they just go in my general blob.
Also, if you're planning to use them, adjust your "engineers auto repair" threshold, otherwise engineers will ignore these guys.