Doing hundreds of batches means you will be in business. I would not be impressed with a "professional" soap that had lumps in it that didn't have its color or fragrance all the way through. I don't find that to be a professional look, it simply looks like it was tossed together by someone with not enough time to do it properly. I consistently heat my MP so it is completely melted, and I have minimal bubbles. What few bubbles I do have are easily taken care of by ONE spritz (per bar or two, depends on how they're spaced out) of 91% alcohol from the pharmacy department. I always get more bubbles when I stir harder or use something that incorporates more air like a whisk.
And by the time you get to the point of making pounds and pounds of soap in a day, you won't be using a microwave - you will upgrade to using a melting pot much like what soapequipment.com sells. Measuring out the MP needed for each batch, then having to melt each batch separately is going to be a giant time suck. However, the extra 10-20 seconds it takes to completely melt the lumps will make your soap seem more professional.