It's expensive to have boards assembled for you, particularly in small batches. How many are you getting made? 10? 100? 1000? Some of the larger PCB fab houses offer assembly as well, but the prices are eye-watering for small boards, because they have to make a stencil and all. A while ago I found a site that gave price quotes for that, though I forget what site it was. Basically, for small lots, the assembly will cost more than the parts. You look at the dirt cheap boards from china and think "look how cheap that HC-SR04 is, and all those parts, it can't be too expensive to have a board loaded for me" - but those are produced in lots of tens of thousands, using a design that's been in production for years.
Also, cloning the Yun is a lot more difficult than cloning a mundane arduino board - that WiFi section has fancy stuff under the hood, and since it does WiFi stuff, you might need to go through a certification process to sell it (not familiar with the applicable laws, but people on kickstarter always complain about the fcc certification). I wouldn't recommend that course of action - making a shield that you'd stack onto the yun would be much easier, and probably cheaper overall. Or, convert it to use ESP8266, and then roll your own arduino board and leave a header for plugging in an ESP8266. Either of those will be a much easier board to make.
Also - With boards, size is money, and 3x5 is huge, and in fact you won't even be able to design a 3x5" board in the free version of Eagle (that won't let you do any dimension larger than 4"). Do you ever wonder why all those chinese modules have everything crammed into a postage stamp sized board? For small run prototype, most of us use OSHPark, since they're usually the cheapest; from them, a 15 square inch board is $75 for three boards! ($5/square inch gets you three copies of the board).
I haven't seen any proto shields that would have a good spot for a DB25 connector on them, but that doesn't mean they don't exist. For first gen prototyping, I'd just solder wires onto the connector and run them into a 0.1" dupont connector that's real easy to connect to the proto shield.
In any event, your fear of SMD soldering will be a problem unless you have money to burn, because you'll need to solder up a prototype board to verify you didn't make any mistakes in the layout or design, before you send it off to make in quantity. But if you want to make it in quantity using throughhole parts, you'll take it in the wallet - assembly costs for throughhole parts are much higher. If you're not willing to do SMD soldering, you really limit yourself. All the best parts are SMD *, and they also take up so much less board space. Also SMD soldering really isn't that hard if you don't use the smallest sizes. The resistors and caps are by far the hardest part, though 805 and larger isn't that bad to do by hand.
*try to find a MOSFET that works at 3.3v gate voltage in through-hole, then try to find one that works at 1.5v in SMD, and you'll see what I mean. A lot of the good stuff is only in SMT now.