Well, that does tend to make certain things easier, yes.
If you compiled them into a hub, though, then you don't start off with the glowgem and spy-eye.
That's good, too, because I use the lamp in my hub.
Exactly why, though, I'm not sure...
I guess I just felt like they weren't used much.
Not as if they really add much to the game - in fact, to some people, they might be annoying.
To me, it kind of adds a very minor time limit to dark levels, and as such, I plan to have several power cube refueling stations throughout the game.
Oh...
but, er, yeap, back to the point, I do agree that if you plan to have sections unlocked by obtaining the tools, it may prove to be a bit less easy - or scary - than you had originally wanted.
(Though Kooky's The End 7 certainly proves quite the exception.)