I only have about a week under my belt with this game, and largely with ver 1.02, but I'll give my .02 as see it currently.
1) My simple answer on units is that you can only buid what you can afford. Early in the game, when you are trying desperately to expand, and build enough defenses to keep what you have currently colonized, and research, it's a bit of a tug of war for me. I usually end up having a small fleet right away with a cap ship and 10-15 light cruisers for clearing out the systems for colonization, then as soon as I can, I ramp up another fleet for defense purposes and continue to add to those fleets as I expand outwards. For me, it's not till mid to end game do I have enough resources and enough access to the better units to really have a third fleet. Usually by that time, I am on the offensive and I use that third fleet to box in my oppopnent (since he tends to rabbit every time I show up with my main fleet). That way, he jumps right to my other waiting fleet.
Playing with pirates enabled tends to be more problematic in that I have to "Fleet up" a bit faster just to defend my early gains, but then my research tends to suffer as a result.
That's a bit of a broad answer, but it's what Iv'e been running into.
2) With regard to surplus, for me that tends to shift depending on what part of the game I am in. Early game I always have a shortage of crystal, and more credits. Occassionaly I have run out of metal too, but that depends on your planet makeup. If I run across a volcanic planet or two, then that may not happen, as they give me 3 metal resources. Same for an ice planet, as they give tree crystal mines. If I end up with all asteriods, then I'm almost always short on crystal and metal early game.
Mid game tends to be a surplus of cash, and just barely keeping up on crystal and metal.
End game tends to be LOTS of cash, a fair bit of metal surplus and again, just keeping up with crystal.
3) On expanding and colonizing asteriods? Always. Bottom line, you need as much crystal and metal as you can get. The more/faster you get crystal/metal, the faster you advance tech and your ability to maintain and build fleets, let alone research.
4) I don't think Iv'e ever had more than three fleets at one time. Keep in mind that to date, Iv'e only played random small maps to get a good feel for the game mechanics. That strategy may not hold water when I move up to medium size maps and have more enemies to deal with and/or more territory to cover.
Hope that helps.