I have thought about the water ingress when I installed my Wallas..... wallas does make a closable vent for the purpose, but you cant use the heater with it closed, but I didnt go with that option, but instead have the regular vent...
I think the only other way is to build a modified Dorade box for the vent, but without some thoughtful modification, one may have trouble with using the heater due to the exhaust venting out the middle tube, with the fresh combustion air being brought in thru the outer tube.... with too much restriction, the outlet and inlet might not have enough separation, and so the unit may ingest too much exhaust with its combustion air.... and so become very inefficient in its fuel burn... its just something to think about.
when I did my installation, I used extra vent tubing, and from the heater I routed it down and below the elevation of the heater, then turned and went up as high as possible into the gunnel area, then back down to the vent outlet/inlet..... then I made a 1/4" hole in the bottom of the outer tube at the low point.
the theory is, that any water that goes in the vent will be metered due to the size of the vent opening, so it wont be much, and then it will have to make its way upwards about 12inchs thru a tube that has an obstruction from another tube inside of it (the exhaust), and if any water makes it completely over the top of the loop, it will run down in to the sag and drain out the hole I made in it..... and hopefully never make it up to the heater unit.
I am not sure how yours is installed, but I think I have a good thoughtful installation, and the only thing I can think of that would make it more secure and still always be available for use, is to have an open shield over the vent (but open on all sides) so that a direct shot of water from a wave (or fire hose) could not force its "pressure" directly into the vent opening.... and a glancing shot of water wont allow much into the opening to do any harm if it was installed according to the instructions with the heater.....
I have my vent installed on the rear quarter about 5" below the rubrail, which is highly recommended by wallas, rather than out the stern of the vessel.