Well, depends on your version of efficient. A soul frame uses a lot less rare resources than ender pearls or uranium. It also lasts for many many breeding cycles instead of using a unit every single time, they also reduce lifespan as a bonus, speeding how fast you work. If you mean efficient in number of blocks used and thus cost in gold to make the frame housings (or diamonds for mutators), your right. By nearly any other metric though mutators are the wrong way to go.
In my set-up it's the other way around. Although in response to your comment without the systems I have in place, yes you're right.
I've got a breeder alveary, so in that i have five mutator blocks with ender eyes in each, and then six frame holders with chocolate frames in each. This means that any bee I put in there has a 100% chance to mutate and 1 life cycle.
I started off with a blaze spawner, and an enderman spawner, both are fairly easy to make, just time intensive on the enderman one. So thus I have a renewable source of eyes of ender. Considering you don't automate a breeding alveary, then I think mutator blocks are definitely the way to go once you've got the infrastructure.
You are correct in saying that they're less efficient in terms of without automated systems. But you can make automated systems for the mutator block resources, and cannot for soul sand (That I have found). So once your base is up to the stage of "Automate all the things~" then mutators are the way to go.
So, soul frames to start off with, moving onto mutators afterwards.