It really depends. In a lot of cases, there's no need to make a ReferenceAlias for an object/actor provided it's already persistent. Most actors and doors, for instance, are already persistent so you might as well just set up properties for 'em. If pointing a property at something that
isn't persistent by default, why that'll make it persist forever in users' saves and would be a prime candidate for use as an alias that it'll cease to persist in the absence or completion of your quest. There is still a "Persistent Reference" flag for all cell children, it's just not visible in the CK. =/
I guess if you *don't have a way to check, go with an alias unless it's a door or actor as they'll already be flagged as persistent. You can also "Use Info" and see if it's referenced by another form's script as a property. If it is, then you'll know it's persistent.
*When TES5Edit is out, this sort of stuff will be a lot easier to determine.