I just use D-Pad just in case because all pad players use D-Pad, but I honestly notice no difference between the two.
Yes, and you’re going to be doing a hell of a lot of it. Not necessarily to learn to do specials/supers/ultras (although you’ll spend a good few dozen hours on that alone before you’re at a level where you can do it anywhere near 100% of the time), but for learning combos in ANY FG. In SSF4 things like 1 frame links will take you so long practicing muscle memory that you’ll want to throw your stick. Repeatedly. Until it’s a broken up pile of plastic and electronics.
As far as playing online goes, with stuff like 1 frame links where timing is so strict, you will not be hitting very many combos online. You can learn the basics like zoning, matchups and the like online just fine, but when it comes to playing at a higher level, i.e. reacting to your opponents moves properly where you have a very small time frame to do so and knowing what combo/move to use in said situation and BEING ABLE TO DO SO WITHOUT THINKING ABOUT IT, well that takes a whole lot of time offline playing with other people.
When I say online is alright, I strictly mean playing against people who you know are good and training with the same group of people. Playing ranked matches is BAD, you only encounter scrubs who just rushdown or turtle and throw out random specials. Most player matches are similar to this as well.