A little sandpaper goes a long way towards breaking the edges of cut glass to prevent cuts.
THe thing to keep in mind in a sump application where you are using a pre-built aquarium and installing baffles is that really all you need to do is put enough silicon in place to structurally hold the baffle and make it "mostly" water tight. Small leaks here and there aren't going to matter much, because the flow through any sump is enough to overwhelm the any leakage and spill over the top of the overflows anyway... in other words, when you are using a baffle to divide two compartments, both with water, what does it matter if 1% of the water leaks through and 99% goes up and over like it's supposed to...
When installing acrylic baffles, I usually use a TON of silicon... a huge 3/4" bead on each side of the acrylic, to lock it in place. I've never had a problem doing this. The trick is to use thick enough acrylic that flexing is not major. If the baffle flexes under the weight, it can pull hard enough on the silicon to break the weak bond between the silicon and the baffle. Once this happens it's only a matter of time before it fails entirely. I never use anything other than 1/4" acrylic for baffles.
A good adhesive that bonds to glass and acrylic is Marine Goop or Locktite Marine Adhesive and Sealant. You could use small amounts of this to structurally bond the baffles to the glass, then follow behind with silicon to form the seal. You could use this stuff for the entire job, but it gets expensive, and it's very difficult to remove should you ever want to reposition your baffles.