How many shortcodes are too many? That depends on factors such as what else has to be loaded and how important it is to you to shave off every millisecond of page loading time that you can. As a ballpark, a few shortcodes are ok; a couple dozen are probably going to cause problems.
Use global rows or modules instead of shortcodes when you can. Global rows and modules become part of the main layout, so you don’t need separate queries for the data and separate assets to render them.
Beaver Themer is often an easier and better way to inject content into posts and pages than Beaver Builder shortcodes. Using Beaver Themer, many of the fields in your standard Beaver Builder settings have links where you can create field connections, which essentially use a variable that inserts content based on the value of a WordPress setting or a custom field for that page or post. See the examples in the last section of the shortcodes article for a few specific examples.