Drilling hole in Aluminum i-Beam - weakening
The reason an “I-beam” works so well is that the “meat” (strength) of the beam is in the flanges, NOT the web. 

Drilling a large hole(s) in the web will not decrease its strength, especially if it’s in (or near) the neutral axis. I’d keep the hole away from the flange’s connection to the web. I’d also leave about 10x the thickness of the web between holes. 

BTW, don’t let the bolt rest on the flange.