Why does my GPS and Wi-Fi work inside a sealed copper clad box?

Even if you have good contact points every cm or so, if your antennas are very near the gaps (a few mm), the RF energy will come inside strongly.

Some months back, I answered a question about "why metal cages around IR receivers".

Why are many IR receivers in metal cages?

Reading Richard Feynmann's lectures, I found the attenuation is 1 neper (8.6dB) * 2 * pi * wavelength/separation.

Thus a 3 mm wire grid (making the Faraday Cage) with the antenna 3mm inside the grid, has attenuation of e^-(6.28) = 1/533 or 54dB.

For the box to be an effective Faraday shield, the entire peripheral of the top lid must be in electrical contact with the rest of the box. Failing this, RF can easily couple from the largely isolated plane of the lid to the internal electronics.

Also don't overlook the large opening you have on the side of the enclosure. I doubt it would allow the GPS to work but it could enable the ingress/egress of a 2.4 GHz signal.

There are two big gotchas here. The first is the lid issue. The lid needs to be well connected along the entire edge. The easiest way to do this is to use some copper foil tape.

The second issue is that you have wires penetrating the cage. Any wire or cable going through a hole will act as an antenna. Holes by themselves are ok as long as they are small it is the wire that is the problem.

Presumably you need wires. There are basically three ways to get signals and power in and out of a Faraday cage. First is to use optical fiber. This is simple and effective, but expensive, non standard, and either slow or really expensive. It is also hard to send much power over fiber.

Second is to add filters to every wire in the form of a capacitor or pi network to the shield right at the point of penetration. This is good for power and low speed signals like serial ports, but not for high speed.

The final way is to use shielded cables and connect the cable shield to the enclosure right at the point of penetration. This is what you need to do for high speed signals like usb or Ethernet. If you look at the IO panel on the back of a PC, you will see there is a metal piece with cutouts for the connectors and spring fingers. The purpose of that piece is to electrically connected the connector ground shields to the chassis. Without it, the shields would only connect to the motherboard ground and shielding would be compromised.