Hi Iain,
As far as shields go, they are often bulky, inflexible and can be expensive. Making you own board is far better - I do hope it goes well.
The main thing I was suggesting was that you have a look at the shields that are out there and check out how they wire up the driver chip - e.g. simplifying direction control and extra protection diodes.
Where shields and modules are good, is to help prototype a circuit and allow you to get started on the software. They allow you to wire up a system using known working parts, that you can then swap out for your own circuitry as it is built.
Wiring the batteries in series will give you 18 Volts, this sound a bit high - but obviously it depends on the motors you are using. The L293D has an absolute maximum rating of 36V, so 18V is not a problem to the driver chip.
Remember that wiring in series will not help deliver more current to the motors.
Be very careful if you decide to wire the batteries in parallel (to increase the available current), rechargeable batteries have a low internal resistance and if you try to join two batteries in parallel, any difference in charge level between them will result in current flowing from one to the other. This may cause heat and damage to the batteries.
My buggy uses a block of 5 rechargeable NiMh AA batteries in series, I found these are good for driving 4 modest motors. 5AA cells probably take up less space than 4 PP3 cells, and are cheaper! Obviously I don't know the actual requirements (voltage and current) for your motors.
I see you have another post talking about PWM, so I won't mention it here, but why are you trying to reduce the number of connections to the Netduino? I take it you have some cunning plan in mind for the other pins....
Have Fun - Paul