Should formatting affect grades of student essays? I helped my friend, who never used LaTeX before, to convert her PG Diploma essay from a Word document into this system (for a molecular biology class). I convinced her that, with some learning, she could later produce better essays with LaTeX in shorter time, focusing on the content without worrying about the layout. 

But she started to worry from the beginning.

She commented on the placement of large figures and tables which didn't fit immediately at the positions and pages where they called out. She was particularly concerned that these floating figures (placed professionally, I think, by LaTeX at the top of the following pages) "appeared in the wrong places in the middle of the next sections".

I explained to her that these automatic placements by LaTeX seemed "perfect" and  "optimal" to avoid large white spaces left at the bottom of the pages; and that this approach is what we see in most professorially typeset materials (e.g., journal articles, and my thesis ;)). 

However, the professor who later marked the essay commented that these positionings "look odd" and "broke the logical flow", and he seemed to prefer the "inline placement" of figures and tables. My friend now thinks that some points were lost because of this.

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Should (such) layout and formatting issues in general affect the grading of student essays?

If yes, I assume this professor might not be familiar enough with professional typesetting practices, or he simply didn't like what he saw in the essay. Is he free not to accept the common professional typesetting practices in his course?
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.