I drilled 1 3/4" holes thru both port and stbd stringers to run fuel lines, steering cable, control cables and wiring from my center console to the motor etc. After passing thru the stringer, they travel up the sta 6 framing in an enclosed chase up to a sub-shelf along the underside of the of the shear deck. The only place these cables and fuel line show is at the transom where they exit the shelf and run to the motor.
As Bob says, you can run these things thru a chase under the deck between the stringers back to the transom, but in my boat with a belly tank between the stringers, I had no room in there for a chase.
Cutting a hole in a stringer doesn't weaken it as long as you leave 2" of wood above and below the hole. Any good plumber will tell you that. For peace of mind, I backed up the stringers' holes on both sides with 16" x 3/4" ply glued and glassed to the stringer.
The problem I foresaw with running a pipe chase under the deck to the transom where it elbows up to the motor is keeping water out of the chase. It seems like once it gets in, it's there until it dries out unless it can drain into a sump area at the transom. My boat has a sealed deck and no sump. This way I don't need a bilge pump which was a prime consideration when planning the layout.