The rudder lines are supposed to enter the hull through tubes located at the stern. The tubes have an external end cap with a hole for the line -- they sometimes were pulled out of the tubes by the action of the rudder lines. The old tubes were drawn up to the underside of the rear hatch with the idea of keeping any entering water from extending past this point by gravity. In rough water this didn't always work. To make matters worse, there is an indentation at the stern where the lines enter (on the old Adventures) that collects standing water (subsequently redesigned).
New tubes were developed a couple of years later with internal seals. They are an improvement but not perfect. If the water is bothering you, you can order a universal line and tube
assembly kit -- look on pg 48 of the online Hobie parts catalog for the part #. This should greatly mitigate any leaking from the lines. Before you order, look over the installation and make sure you can reach all the tie points.
If only your caps are missing, it looks like you can order new caps (same page). You will not have sealed tubes though and the caps can be rather difficult to poke the line through. On the kits, the lines are pre-inserted through the tubes -- much easier to use.