I remember back in previous editions, the magically inclined received a penalty. Does this apply in 4th edition, or am I just living in the past?

No, there is no penalty. IIRC, that penalty was dropped in SR2.

In fact, adepts can enjoy a significant boost in the SR4 matrix, leaving many normal deckers in the dust.

Like with most things, an adept who focuses on a task will be insanely good at it(thats kinda the point), though a mundane using those same BP on skills and resources(especially 'ware) will most likely be more rounded. Adept hackers are usually the best around(save a technomancer who's been around the submersion block a few times), but a mundane hacker can easily be good at combat, B&E, subterfuge, or whatever they want.

Heck, magicians can be great hackers too, they just rarely have the BP, nuyen, or karma to get good at it, especially since you can't cast spells in the matrix.

It's actually harder to be a dual-purpose decker in SR4; you have to invest much more heavily in the necessary skillsets. An otaku has an even worse time of it: even with a few grades of initiation, the adept will have gotten better as well. In fact, since Improved Ability costs half a point, pound for pound the adept will gain more ability for the same amount of karma.

You could do the over-the-top Adept-Decker thing in SR3 as well.

True, but it was much harder to outdo the otaku. Considering that they could start with a skill of 8, the otaku had a definite leg up on the adept decker.