Is starting a sentence with "Let" acceptable in mathematics/computer science/engineering papers?
These are all acceptable. My personal preference would be to reserve &quot;let&quot; for statements that are (essentially) assignments, like the second one in the question. The other two establish notation conventions. I might say something like

We use lower case letters for scalar variables.

or

Lower case letters represent scalar variables.

and

We write R for the set of real numbers.