There is not a significant difference between the two sentences. The sentence with the word “having” is a little clearer though. Given that, among the two choices I would prefer the sentence “Who is really benefiting from having volunteers?”
This said, I would honestly not say that either one of the sentences sounds very natural. This is primarily because the sentence needs a qualifier before the word “volunteers,” such as “the” or “a few.” This is not grammatically needed, but would help the sentence feel more natural.
Additionally, the use of “really” feels excessive in the sentence. Though word is successfully adding emphasis, it does not feel natural.
I will provide a few examples of how I would suggest the sentence to be written instead:
“Who is benefiting from the volunteers?” ← Notice the word “the.”
“Who is benefiting from having a few volunteers helping out?” ← You can end the sentence after the word “volunteers,” but the words “helping out” provides further clarity.
“Who is benefiting from the help of the volunteers?”
If you would like to use emphasis, that is ok, but I would suggest the word “actually” rather than “really.” For example:
“Who is actually benefiting from the volunteers?”
“Who is actually benefiting from a few volunteers helping out?”
“Who is actually benefiting from the help of the volunteers?”
The example sentences I provided all carry roughly the same meaning. The significant difference is the use of “actually” or not. When the word “actually” is used, it places more of a focus on the word “who” and suggests suspicion. It would be implied that the person asking the question believes the answer is “no one.”
The word “really” and “actually” carry the same meaning in this circumstance, but the word “actually” feels more natural.
I hope this helps. :) If you would like to practice speaking, please feel free to look at my teaching profile and class offerings.