I had this problem as well. What I found was that my load distance doesn't save in V27 and I have to change it back to 99km each time that I want to use the missiles. I can't guarantee that it works for you, but it did for me. Just in case, make sure you have the latest version of the missile pack as well.
I attempted to add this mod into my already running space program. My original thought was to put myself into a position where the commercial missions are used to finance the rest of my program. Everything was going swimmingly until a separated tank knocked out a main engine. That one failed launch set me back so far that it is easy to see that I don't have time to grind back enough funds to support three space stations and multiple interplanetary probes that I have scheduled. The only way that I really see that scenario working out for me is if the client paid for all costs and I still get the full award for successful completion. This isn't to say that I don't like the mod. I've copied a separate KSP folder just to run this. It just can't fit in with my sandbox.
Not necessarily. If you build a small, cheap craft, then yes. If you aren't skilled enough, or confident enough, then you may "over-build" and get considerably less of a reward. If you really over do it, you could even lose money.