At the present time, I'm slowly trying out quest making and have already made my first working one(although I'm still trying to figure out some things).

I understand this much about reference alias for actors..but I noticed you can't make a reference for actors that are not "unique".

Like say I want to make a quest where I'm to kill all hunters, I can't seem to make a reference alias for them.

Do I have to write a script?

If I understand you correctly, you will need to add the hunters you want to reference in your quest to your Aliases in the quest you are making.

Do you mean, kill all the hunters in the whole gameworld? Or just in a single location?

In general, you can use "Find Matching Reference" to find a matching non-unique NPC based on conditions, like their faction. However that does still require that either 1) their location be currently loaded or 2) they be persistent.