That doesn't make sense, Bill
It doesn't make sense that a line for the intake vented loop would come up from beneath the sole, 'cuz both ends would be attached to the toilet--the line TO the loop connects to the pump...the line FROM the loop connects to the bowl. Even if the PO put the intake loop in the wrong place-between the thru-hull and the pump--there'd still be only one intake line...the line coming from the loop would be attached to it and the pump. Same is true of the discharge line...the line TO the loop would be attached to the toilet discharge fitting on the toilet, the line from the from the loop would connect to the discharge line...no need for a second discharge line. However, if there had been a y-valve--now missing--in the discharge line, one side to the tank, the other side to a thru-hull, that could explain two discharge lines going through the sole...they'd both connect to the y-valve outputs...the hose from the toilet TO the y-valve could be missing. And, if the PO had installed a separate flush water tank (or, hopefully not!), a line to the fresh water plumbing and one to the thru-hull with a y-valve in the intake line to allow the choice between flushing with fresh water water or with sea water, that COULD also explain two intake lines. That's unlikely, but I've learned never to rule out any possibility, because owners--especially engineers--can be VERY creative when it comes to designing complicated solutions to simple problems.