Sec Officers:
Many exist
More can be sent by centcom if you increase job slots
More can be hired from crew, and the extras can do the job just as well
Many copies of their gear exist, and more can be obtained
With Chaplains:
Only one exists
You cannot increase job slots to hire more if that one is permanently lost
You cannot hire them from crew either, because while you can give them the job title, the job title does NOT confer chaplain powers
Only one copy of their gear exists, some of their gear becomes unremovable once equipped, and getting replacements for their gear is difficult
Practically, chaplains likely have special knowledge of how to use holy water that the average sec officer does not have
Given the great disparity above, it simply does not make sense for the chaplain to be wandering the station during cult/vampire rounds.
They should stay in sec, blessing water tanks, administering doses of holy water, and helping protect the brig.
Yes, they might be able to help on the front lines, but:
They're effectively impossible to replace short of admin intervention, and your anti-cult/vampire efforts will be severely hurt without them, so... can you really afford to risk losing them?
They're quite likely to be a target of the vampires/cult. So... they may need to stay in secure areas for their own safety.
If they're killed, and sec doesn't realize it, a fake replacement chaplain can do an insane amount of damage, for example, by providing fake holy water that enables vampires/cultists to avoid being identified, or even escape.
For all of these reasons, chaplains shouldn't be going full crusader during cult/vampire rounds.
If they want to help, they should be staying in the brig, assisting with prisoners, while sec watches their back.
Going rambo as chaplain in these round types can really cripple the station's ability to respond to threats.
If you die... that's it. You probably won't get replaced, and nobody else can do your job.
The only big reason to leave the brig as chaplain during confirmed cult/vampire rounds is to use your book to erase cult runes.
That can be a major help, and is worth doing... but you should probably take at least one sec officer with you when you do so.