Should formatting affect grades of student essays?
Is LaTeX better than Word? This is a holy-war kind of a question. I personally agree that LaTeX documents often, but not always, allow to produce a better typeset document in less time (as soon as you know enough of it to write the document, and do not spend time googling for "how do I do X in LaTeX"). 
Are LaTeX's floating objects perfect? Some things are less than perfect even with LaTeX, and handling of floating objects is one of them. You can suggest using [p] instead of [t]/[b]/[h] options --- this can still generate under-filled pages, but at least it looks like it is done on purpose. 
Should you Professor comment on the layout? The way how the document looks definitely affects how it is perceived by the reader, so if something looks weird / unusual, it is all right for your Professor to comment on it. 
Should the layout affect the grade? There is no general answer to that. Some Universities even have a very rigid guidelines on layout for theses submission, which sometimes, sadly, prescribe the use of Word, and sometimes, conveniently, the use of LaTeX (particularly if LaTeX is taught as a part of the Program). In this case, of course, students can be penalised for not following the guidelines. Sometimes points for "presentation" are included in the task specification --- and you can lose them if your Professor decides that bad typography affects the presentation of the document (I don't think LaTeX can be that bad, though). However, Professor should not simply reduce the grade if they feel that the layout is unusual.