The wiki might help you be more comfortable designing ships-as well as discovering what bonuses actually exist where and what they do.
That loophole in spying is still in and to my knowledge there is no immediate intent to fix it, either.
Yes, sensors, logistics, and speed do not operate on a percentage basis, but an absolute. I can see how this might be confusing, but to be honest it's never been an issue for me. Technically miniaturization also operates on an absolute basis as well.
Social production, as you stated, no longer goes to waste if unused and is funneled to military (but if you are building a social project on that planet, this doesn't happen). It's not "excess" production transferred. While overflow military is paid for with no compensation or return on investment, I have to try to have a game and a setup where this is actually relevant, as I'm not producing ships on each planet each and every turn, but your mileage will obviously vary.
That isn't to say I wouldn't like to see it fixed, but I don't know how high of a priority it is for either the player base or the devs, really. The simplest solution would seem to be to have only the used military production be charged (for instance a 110 industry capacity world, for ease of example at 100% funding with no bonuses, producing a 100BC ship, would only utilize 100 industry and therefore cause the player to pay 100BC as opposed to 110BC for that planet for that turn). This would seem to work even when the overflow is on the 2nd, 3rd, 4th, etc turn of a ship build as well.
Interestingly, overflow social is charged as well (building a 50BC improvement at 18 industry a turn will cost you a total of 54BC), but people tend to not complain about it so much. Perhaps because rush buying an improvement over an existing one takes into account not the improvement cost, but how much production was actually spent on it, but maybe for other reasons as well.
Social, military, and research bonuses all give half of their bonus for free. I'm not aware of any other bonuses that you would have to pay for.
Many people have complained about the racial spying ability, but it hasn't been touched, either.
As far as bonuses go, it is important to remember that your civ-wide morale bonus deteriorates as a function of your population on a per-planet basis, and planetary approval is then further modified by tax rate, which, while non-linear, is a set amount not modified by your population, nor anything else.
If memory serves, a starship bonus gives ships built on that planet more hp. If you never built a ship there, or only built a couple, you probably never would have noticed it-particularly if they were tiny or cargo hulls.