As others mentioned if you have the electronics skills then there is a lot you can do. If you are going to follow a path that somebody else already took then you have three choices from what I have seen
1) NAND bothering. Mainly backup and restore of your own NAND images to dodge unwanted updates and whatever. Some also used it to also roll back saves (saves might have been noted in the NAND) but that is less useful now. Also others would unlock the NAND after gateway decided deliberately bricking things was acceptable behaviour.
In the extreme we did also see a NAND and CPU transplant which allowed someone to get a true North American n3ds in a Japanese non XL shell
http://www.noodlevisions.com/?p=10
2) Control fiddling.
Read the control inputs out, remap buttons around if you can not be bothered to softmod a game, the usual suspects of turbo fire, premade button combos, something a bit more exotic (my favourite was someone attached a camera to a control setup to detect when they encountered a Shiny pokemon as it took a little bit longer to load the battle).
3) Video capture.
Loopy and katsukity being the main two people to do anything here. Afraid I have not followed it for specifics but it usually comes in kit or send it away form. You could probably build your own as well as the screen protocol does not seem terribly exotic.
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Sound was mentioned above. I have not seen a true hardware hack here -- most of the time it has come up we tell people to get a small amp (they are a popular beginning electronics project) and stick that in the headphone socket. The idea being that depending upon where you are in the world (definitely France, usually then Europe and it not a bad thing so it can go worldwide) the headphone socket output might be limited by law in the volume it can output as all the kids were killing their ears with headphones. Altering this sometimes means you delete a component, other times you change a resistor value/input on an amp and other times you have to bypass the lot and do something else yourself.
I do not know what was done as far as RAM reading/writing mods behind closed doors for the 3ds and for the effort right now I would probably just find a softmoddable 3ds.
In the future the sky is the limit. The so called enhanced flash carts on the DS quite notably added serious external processors and ran code on them but the concept is hardly new and goes back as long as any kind of digital or mechanical logic really. I would be interested to see more hardware firmware/homebrew hacks but I am not sure it worth the effort working one up -- even if we still needed 4.5 3ds there would probably still be enough supply if I was weighing up the effort.