Can I change the size of my applications folder icons from the dock?
To change the size on the Applications Dock menu in Grid view click the Applications Dock Tile and then press command- to make the menu and icons smaller or command+ to make the menu and icons larger.

I have tested this under OS X Mountain Lion 10.8.5, OS X El Capitan 10.11.6 and macOS Sierra 10.12.

The image below is from OS X El Capitan 10.11.6 taken on a Thunderbolt Display at 2560 x 1440 and of three separate screen shots that were cropped from the lower right corner to the size necessary to show the size of each grid menu and its size changed and layered to reduce the size of posting 3 individual images. Nothing has been retouched, just cropped and layered to contrast between a large menu in the back, the default size menu on this Display in the middle and a smaller sized menu up front. Calculator.app was used to show scale and as you can plainly see the size of the icons changes with the size of the grid menu.