Well yeah, but if you mod the cart then you've ruined the cart.
and if you hack a console, you've ruined the console!
Aside from that, modding the carts would make the whole ordeal even more impractical. You are telling me you are going to break open your three dozen+ cart collection just so you can play them on your custom portable? And if you are just going to play a single game then what would be the point?
I agree with you where you look at it in practical way. But the point is not about practicality. And no, if I were to do it (which I wouldn't. The console mods are a bit techy for me) it indeed would be a lot of work to hack a whole bunch of carts. But using the N64 example, to answer two points you raise, IF I were to do it, 3 carts would be sufficient- Goldeneye, Ocarnina of time, and Mario64. Maybe also Mario kart 64. That's all you would need to have a presentable system. If you include a fourth, isn't that TWICE as many games as what the N64 had on launch?

My choices answers another point. Rarity. Yes you would indeed be retarded to mod Sin and Punishment. But how many millions of the above titles were made? Are the same number of millions still being played? I don't think hacking 4 carts is going to impinge much. It's not going to swing the balance the other way, unlike say Model T Fords. I bet there are more T-buckets out there, than actual T models nowadays...
You are right, none of it is really practical. Hobbies needn't be. All the consoles Ben has hacked, for me, demands a lounge chair

In which case it's better that it just sits on the floor connected to a telly.
Oh, and by the way, I hack Atari Jaguar controllers. That would definitely fit in the rare category. And despite my argument, they are hacked for practical reasons (although I would to think I have incorporated form and function). However, just one supplier of vintage atari stuff has over 4000 new ones in stock. So rare doesn't necessarily mean valuable...