You do this from the web frontend on the 8beta9. Log on to you pi from another computer. Along the top are some tabs, click on "database admin". Then on the left should be a tab called "menu items". In there will be a list of all the icons that show up on your pi. Edit the ones that you want to hide and change the visibility from a 1 to a 0.

I don't have my arcade turned on right now so the names I listed may be a little off.

Hope it helps.