Working out ballast tank volume is a frequently asked question. The simplest way is to ask someone with the same model what volume their tank is, or perhaps Bob at OTW can give you some pointers, as they supply a wtc/module for this boat. I would think it will be somewhere in the region of 1.5 litres, but that's just an estimate.
Using weight is a bad idea for calculating ballast tanks. You need to think about displacement.
For a start it's difficult to weigh just part of your model, unless it happens to conveniently split right at the required surfaced waterline. Secondly most materials used in model submarine construction are denser than water e.g GRP, metals etc. Thus if you use weight as your method, you will tend to wind up with a ballast tank larger than required, which is better than it being too small. But if it's a big margin of error, that means longer filling times, more power used etc. Conversely, if the model is made from wood, the tank will likely be too small-, and the boat will not make a scale waterline.
Many thermoplastics like ABS , polystyrene, PMMA etc. tend to be about the same density as water. If your model is constructed from one of these, and the shape is relatively straightforward e.g. a cylinder then you can probably work out the volume of the tank using a bit of maths.
However a boat like the S-class is not a simple shape, plus it uses mixed media- brass decks and hand laid GRP, the latter tends to have a variable thickness owing to the nature of construction, which complicates matters further, and brass is more than eight times the density of water!
The most accurate way to find out the right volume of tank for this boat (and just about any other sub) is by empirical means.
Build the boat up, sans paint etc.
Put it in a test tank, and being denser than water it will sink. Add buoyancy- polystyrene foam is the best material to use. You will need to make a cradle of some sort to keep all the foam in place. This can also be made from foam, as it doesn't need to be super strong, but you should ballast it down so that it is neutrally buoyant, else it will skew your result.
When the boat is neutrally buoyant. e.g the boat sits just on or below the water surface, add more buoyancy below the waterline until the desired waterline is reached.
When you reach that point, remove the foam used to get the boat from neutral buoyancy to surface trim, work out it's volume- easiest if you cut the foam in uniform blocks e.g. rectangles. Increase that figure by 15-20% and you have the ballast tank volume required. The extra margin allows for differences in water temperature, extra volume added from applying paint finishes, and also gives you the ability to statically dive the boat by producing a little down thrust.
All this assumes that the WTC sits below the waterline with the boat surfaced.
Once you know the volume, you then need to decide what sort of ballast system you are going to adopt, as this dictates the size of tank needed. In your case we know you are going for a water pump based system. If you are going to be using the nautilus pump, then that rules out a sealed tank, as these pumps can only make 15 psi max, and that will only half fill the tank. With a 100mm diameter cylinder the tank would need to be over 43cm long assuming 1.5 litre volume, and that would pose stability problems I think.
You could go for the OTW type system which vents into the dry space, but I would advise some sort of sensing to ensure the pump doesn't overfill the tank and flood your module. This could be a simple float switch if you don't fancy the electronic probe system.
Another system would be to pump into a vented tank to get the boat to decks awash, then use a smaller trim tank (mounted inside the main ballast tank) which could use any type of ballast system to take the boat fully under. This more accurately reflects fullsize practice.
There are other variations on this theme.