You have one of two different kinds of hull construction. I know that the early Nacra catamarans were solid fiberglass and the hulls and deck were probably about 1/8" to 3/16" thick with just fiberglass and resin (probably thicker in areas like cross beam mounts). The other type of construction, very common in all the Hobies and all post mid-80's catamarans, is "foam core" construction. This has a thin inner layer of fiberglass (probably 1/8" or less), an internal foam core (usually tapered at the edges of the piece but up to 3/8" thick), and then an outer fiberglass layer usually around 1/8" thick or so.

the instructions you got for repairing it "Hobie style" is to repair a soft spot that results from the foam "delaminating" (aka breaking away or crumbling) from either the external or internal fiberglass layer or both. To repair this you drill several holes in the soft spot, twist something around to futher break up the foam inside the area, and then fill it with epoxy or polyester resin to re-fill the middle to reconnect the inner and outer fiberglass layers.

What I suspect you have (again, unconfirmed) based on your drilling experience, is that you have a solid fiberglass construction. Soft spots in this case would mean that the resin and fibers have weakened over time (absorbing moisture, repeatitive stress, etc.) or that some internal reinforcment has broken away from the hull. You will need to either reinforce the areas in which the laminate has weakened or repair/replace the internal reinforcement that has been damaged (bulkheads or stringers). This kind of repair is going to involve cutting large holes in the deck, reinforcing the area, then fiberglassing the large cutouts you made back in place.

Bottom line though, is that we need to figure out for sure what kind of construction you are dealing with. It could be that the foam is so far gone that you thought you went through to the inside of the boat when you have just gone through the first layer...dunno. Could you see light from the inside through the holes you drilled?