The beam intensifier upgrade simply makes mining take less time due to faster disintegrations. The amount of mineral or resource output is not affected.
The upgrade makes it so that more is mined before you have to pause to let the mining tool cool down less, which makes mining large deposits take less time overall.
For a reference, check the wikia, though it isn't very descriptive.
I was curious to see the difference between the Beam Focus upgrades and the Beam Intensifier upgrades so I did some googling and found this:
Intensifier speeds up mining on rocks of resources like iridium, aluminium, and heridium. They're the rock formations that when shot with the laser look like a chunk was blown out of them. They're most commonly the large pillars of rock on a planet that you can mine.
Focus affects the speed of mining for crystals like plutonium and gold, small/medium sized rock formations that contain iron, and plants that contain carbon.
This agrees with a post here as well.