As one who's cut literally thousands of holes in cases over the past 22 years using Dremels, plasma cutters and hole saws from what I see there shouldn't be any issues with barbed ends cutting through the plastic jacketing on wires. A cheap set of jeweler's files work great for deburring as does an actual machinist's deburring tool. The files are a must have for anybody who does case modding. I got my set for $6 from a local hardware store. My deburring tool came from when I worked as a machinist. By far the cheapest and most effective thing to use when worrying about sharp edges is the tubing used in fish tanks with air pumps. Cut it to size then use a sharp utility knife to put a lengthwise slit in it. Slide the slit tubing over the edge of the metal and you're good to go. It's literally dirt cheap and extremely easy to work with plus is a fraction of the price of the plastic runners sold at electronics supply places for the same purpose.
If you're going to be cutting lots of fan holes take a dead fan and cut the center part out leaving only the outer housing. This will be your template for laying out where the new hole is going to go. Use masking tape and a fine point Magic Marker to tape over the surface to be cut and lay out the hole. Essentials for working with a Dremel include the diamond cutting wheel, a set of high speed carbide cutters, the thin reddish-brown cutting discs (the thick ones get too hot and aren't good for fine work) and a couple of spare mandrels for the discs. The diamond wheels come with a mandrel but they get so hot it's impossible to remove the screw even after a short time using them. A good electric drill and a set of quality drill bits are also essential. Use a sharp center punch for laying out corners of rectangular cuts, drill holes in the corners using the divots from the punch as a guide then cut the connecting lines with the diamond cutter. Cut in the direction the blade spins and slowly let it pull itself along, you'll get the straightest cuts this way. Make sure you have the guideline laid out on masking tape on the top of your work surface. Use a ruler to lay out the lines. After a few times you'll get professional looking results.
The diamond wheels are expensive ($15 or so American) and do wear out after cutting a few large holes. I've worn out several but never broken one. The cutting discs are extremely brittle plus break easily and wear quickly. The softer the metal (or plastic) you're working with the faster they wear and break. They're cheap ($4-6 dollars US for 36) and I've been using the ones Walmart sells because they work just as well as the actual Dremel branded ones but cost less. Even after 60+ years of using them I still break plenty of them but far fewer than I did years ago. A steady hand and using the highest speed on the Dremel gives the best results when working with steel. Plastics, brass, aluminum, copper, etc. all cut differently and you'll only learn by practice. The high speed carbide cutters are my main go-to most of the time these days though and a good set is very expensive. I use a Snap-On set I bought dirt cheap from somebody who was retiring from the business in the early 1980's and they're still going strong today. A much cheaper Harbor Freight set should work well for the hobbyist doing case mods though. Practice makes perfect and after you get the hang of things you can also get artsy in the laying out and cutting process.
