Keith,
I think that all of the SMC era Beavers (1995 - 2002) were wired with the Raycor water separator tied directly to the batteries instead of through the ignition switch. So your condition is normal.
As for the need to change primary and secondary filters. The 2 micron secondary (Cat) filter maintenance schedule list a once yearly change, although I do not change mine quite that often. The 30 micron primary filter (filters out sticks an gravel) does not need to be changed that often if you are using fresh clean fuel. As a fulltimer, I change my primary filter about every 4 years. However if you have any fuel issues like water causing microbe growth (commonly called algae) or any other contamination problems, much more often filter changes are necessary.
Gerald