[...] The aluminum frame of the ROV will be connected to ground as well to provide a common ground between the logic circuit and motor/thruster circuit. All wires will be 50' long.
So basically the only ground connection between the power supply and battery pack will be down a 50' tether. Should the grounds as surface be connected as well? Are their any issues with grounding that I am overlooking?
Usually, you'd connect the grounds at the end with the lowest impedance, which is at your power sources, but then they need to be isolated at the ROV, or you'd create a ground loop that could make all sorts of strange things happen to the logics.
In your particular case, I'd connect the grounds at the ROV (since they are already) and only change it if things start acting up. However... With aluminum and water, I'd add a copper wire, as aluminum oxidates extremely fast, ruining initially good connections.
In any case, only connect the grounds in one place!
I would like to make a diagram of this, any suggestions on a free program?
For simple diagram drawings (no calculations, nor any simulation), any drawing packet that you're used to will do (even Windows Paint - if you have lots of patience). AutoCAD and similar programs is shooting way over the target, unless you happen to have a lot of hours under your shirt already.
For such things, I often use Eagle CAD, but like with any other program - if you don't feel at home with them, they'lll usually take too much time to get you proper results.