Personally I prefer the black and white option, you can adjust colours as needed a lot easier and its cheaper to print :)
The one thing about the designs that just feels wrong to me is the angle of the 'C' boxes. I feel it would look better if it was rotated so the current vertical axis is more horizontal. Think of looking down on a 3D plan of a building. I feel it would give a more architectural feel to the design due to the symbolism and relation to buiding plans.
Personally I like canon printers, I've got an ix4000 for quick A3 testing and its a very good printer for its money, I would happily show a client the work produced on it. The more expensive versions are meant to be even better.
Personally speaking it would depend more on the design of the leaflet/webpage as some work better on the horizontal while others on a vertical approach. It may even work to have a 'corner' used to house the logo's.
What I try to do is focus on the main part of the logo and work around that size wise, then try to make them all look equally proportioned.
Personally I would say this issue is the lack of any nda/set contract for what you have done.
You need to talk to the main client or get your boss to do so to get it sorted out as technically speaking without you signing anything your boss has broken his nda.
As to the work, I follow a simple rule, if its not paid for then they don't get the development work (ie 3d models etc) but they can have all the finished stills/animations - however I make this clear at the beginning.
If you have to end up giving all the work to them, I would probably do a password protected zip/rar (multi part to make it harder for password cracking) or something similar. I would also get a contract signed which states that none of the 3d development work etc can be used without your express permission.
