I think you're looking for this section of my blog:
http://christophermpark.blogspot.com/search/label/Programming 
A lot of your questions are things that I'll have to address in greater depth in later blog posts (I only do a few a month, due to the immense time required to create them), if there's interest in the nitty gritty details. But, to give at least basic answers to your questions:
- There weren't any particular problems with the hotseat stuff at all. Pretty trivial, really. I don't know why more game developers don't support this; Age of Empires II did, and then other games that came after pretty much dropped it. You also get really (pardon me, but) moronic types of save systems like the one in Neverwinter Nights 1, which just was essentially a memory dump. To me, this speaks of nothing but poor planning and possibly cutting for scope. I can't stress too much how trivial and simple this is when planned-for from the start. It does make certain things like recorded games not possible (or at least simple) when spread across multiple sessions, but... so? I think that it's just something that pvp RTS developers tend not to care about because honestly who needs to save a game that lasts 20-40 minutes on average?
- Yes, we unit test, we do profiling, and so forth. Though, we don't have any automated test cases that we run for mathematical correctness; we aren't using any testing software or anything. Our unit testing involves a programmer firing up one of several savegames that we keep handy, and looking at profile data, performance, correctness and overall feel, etc. Or if it's a brand new feature, then simply having the programmer fire up a game and test that out in a few situations, etc. We use the prerelease betas for purposes of what we call integration testing, essentially using our core fanbase to help us balance and do the core testing. They don't seem to mind (and in fact seem to really enjoy having input), and it's the only way for a tiny company like us to get by since we don't have a staff of hundreds (or even one or two) testers. The programmers also play the game recreationally, which helps to find things and keep things clean, too. Mostly we have an emphasis on clear software design and bug-avoidance techniques, which also works largely because of the low number of programmers working on it. For things like balance, we do have the simulation that we run for strong/weak data, and we do some computer-assisted analysis of balance with that, but a lot of it also boils down to intuition and user testing because ships can be used in so many nonstandard ways.
- I would definitely not call AI War simpler than most RTS games -- the simulation itself for all the unit interactions, etc, is several orders of magnitude more complex than... well, any other RTS game, I feel confident saying. However, we have no physics simulation to speak of, and obviously almost no environmental simulation to speak of, also. So it's vastly simpler in a few areas (non-gameplay-related, mostly, just environmental), and it's vastly more complex when it comes to the core gameplay itself. These factors don't matter one whit to having hotseat functionality if you design it properly -- in fact, most of those sorts of environmental factors can be completely ignored for most purposes as things like birds chirping or trees blowing in the wind, etc, are typically not synchronous in an RTS game, anyway; cosmetic, non-simulation-affecting stuff is run on an entirely different random seed that is not synchronous, typically -- same for 3D animations for units, and anything else that doesn't affect where stuff is, who lives and dies, etc. There's no good reason not to just re-seed that for anyone who joins late in hotseat play, unless your game architecture is just designed in a nonideal fashion from the ground up.
- For secrets, check out the blog if you want a lot of inside stuff. I don't have anything readily handy to tell you off the top of my head, honestly; I tend to be pretty open about most stuff with the game, so there tend not to be a lot of huge secrets to whip out.
