Using dashes vs. commas in business communications

In your example, the em dashes are used in pairs to set off parenthetical phrases. A parenthetical phrase is a clause that is inserted into the flow of an otherwise complete sentence as an "interruption" that adds additional information. If the parenthetical phrase is removed, the remaining words should form a full and complete sentence on their own.

Despite the name, parenthetical phrases do not require parentheses; they can be formed with em dashes and commas as well, as you correctly state. However, your first example is complex enough that I would probably use parentheses to set off the two parenthetical phrases, to avoid a pileup of commas that would make the sentence harder to understand:

Dean London (a business unit of Centrell) have been supplying permeable products to Caramba Unit (a supplier of biological products) since 2009.

Your second example is fine as is, although commas might improve the flow slightly. Em dashes are often thought to apply more "braking action" to the sentence flow, whereas commas provide a gentler "slowing" action:

This initiative, led by Dr. Reiv Nadar and integrated into Dean's research and design unit, intends to gather post-harvest disease control information.

If you do wish to use an em dash, it should not have spaces on either side—use it like this. In some contexts, you can use an en dash or hyphen instead, with spaces on both sides – like this.