For the enclosure, Bud Industries makes a line of NEMA rated waterproof plastic enclosures. They vary in price from $10 to $50 from distributors like Digikey based on size and rating.
An example box that may fit your dimension requirements is the NBB-10260 (Digikey). It even comes with a clear lid for reading LCD displays if you need to.
An option for getting cables out of a box that I have used in the past is a Cable Gland.
You simply drill the correct size hole in your enclosure and tighten the cable gland around your cable. If you adhere to the datasheet dimensions, it can be waterproof and dustproof.
One popular and traditional hacker enclosure has been the classic metal Altoids peppermint can - to the extent that some products and prototyping PCBs are shaped to precisely fit one.
(Image from Adafruit)
For more examples, see a toy, an amplifier and another, a sound generator, a USB charger, one could go on all day.
A fringe benefit of using a metal can like the Altoids, is EMI / RFI reduction, both emission from poorly designed circuits, and from the outside into the circuit.
For smaller circuits, round metal shoe polish cans are popular, and again qualify as "EMI-Safe Device Enclosure".
(from Wikipedia)
Another "hacker's standard" that has been around for decades is the wooden cigar box. They're sometimes found at garage sales or the scrapyard, in a variety of sizes and designs. My favorite are the ones with a double hinge, and a little metal latch in the front. Back in college, I built myself a bench power supply in a big cigar box, that is still around somewhere.
The fringe benefit of wooden cigar boxes is protection from electrical accidents when working with main line power input to your device.
A third standard go-to option in cases where robustness is not a concern, is the small Pringles or other potato crisps cardboard can. They're especially convenient for cutting holes in, for sockets and connectors. The 2 to 3 inch height and diameter make such boxes useful for circuits with a transformer in them, such as non-switched (good old) power supplies.
Finally, plastic enclosures aren't necessarily expensive: You can sometimes pick up assorted sizes in lots of 5 or 10 from eBay for under 1 US$ a box, and manufacturers offer a variety of standard enclosures starting in the $3 range, probably cheaper if you search around.
Best Answer
You don't drill such holes. Instead, you get a punch. For instance, if you're trying to install BNC connectors you need a 1/2" D punch, such as this...
And yes, they are expensive. Prototyping will use this sort of punch, which is hand-powered. For production you get a punch/die set for a press.