To speak to Dan's points a bit. First I will agree, nobody wants to open a perfectly sealed ebox for any reason unless they absolutely have to. I myself need quite a bit of motivation before I even think of cracking the seal on the ebox. Case in point; I actually have an updated bilge harness* and some new battery cables to go into my ski and I am still waiting for a better reason to crack the ebox seal.
That being said, the sole reason for installing the wires into the ebox is because it is sealed and we don't want to mess with things anymore. Would I crack the seal just to install a bilge kit? Mmm, probably not but if needed to be opened for another reason, then yes I would add the wires without hesitation. Just think, no more extra or corroded wires hanging off the battery, not to mention no more not so waterproof fuse holder floating around getting constantly doused in water.
Now here is where I get to disagree with at least one of Dan's points. The only two points of contact inside the ebox for the bilge are the positive and negative wires. Thus, nothing to service. If these do happen to need servicing, you must have water intrusion and the entire ebox will need servicing anyways. The fuse is tucked under the screw cap and accessible if needed.
Now, If you do have bilge issues, the issue is normally with the switch or the pump. Kits like my Tidy bilge utilize quick connectors so you can swap in a new pump or switch without opening up anything. The way my ski is set up, I can swap out a pump on the beach in under a minute with no tools. The switch can be disconnected from the harness just as easy. (Removal from the dash or bars is another matter)
I moved the wires into my ebox when I built and installed the very first Tidy Bilge setup in 2009. It has not required any maintenance in over 5 years now and all I ride is saltwater. The ebox itself has moved between 3 different hulls and is still sealed and dry. I have changed out a few pumps over the years, making the transition from Rule to Atwood and back to Rule. I also failed the original rotary switch and have replaced it with a first gen Surf Armor switch. Harness and connections are still going strong and I have never had a need to go back into the ebox for any bilge related issues.
*The new harness I have waiting will run one manual pump and one automatic pump wired to a 3 position rotary switch. I really want to swap it over but I also want to see how long the original harness lasts.