No, you won't notice a difference at all. Joysticks are very much a personal choice, and there are LOTS of choices. Bat top, ball top, different switches, tensions.
There are some consensus joys depending on what you want to play:
Hardcore classics players prefer a 4 way, leaf switch stick
Hardcore street fighter players prefer the japanese sticks; either the sanwa JLF or the Seimitsu LS-32. Thing about these sticks though, they are very different than the traditional American sticks. They are a lot more loose, and usually come with ball tops, whereas the American sticks are usually more beefy in feel and have bat tops.
Personally, I think the best joys are wico or happ perfect 360's. If they weren't like 70 bucks a piece and if I could light them, I would seriously consider upgrading my sticks to them.
Here is pretty much the truth though, you probably won't notice the difference. Nobody gave much thought as to what joys were in what cabinets when they went to an arcade, most operators didn't care much either. Whatever you get will probably be fine, and you will probably adapt to whatever you have and grow to like it, unless there is some annoying quality to it; like the long throw of the U360 without a restrictor; or the loudness of the switches; or the clunkiness of a mag-stick.
I grew up in the arcades in the 90's. Pretty much everything I played was a bat top stick. Then I got a hori ex2 for my xbox to play SFIV. The hori uses hori brand parts, which are basically knock-off sanwa parts. At first I HATED the ball top, now I actually prefer it. I still don't like the looseness of the stick, but I prefer balls now. On my MAME cab I have the paradise lit sticks, which are generic fight sticks and I like them a lot. They are cheap sticks, but they are ball tops, japanese style but aren't as loose feeling as traditional sticks.
Anyhow, joystick talk is like wine talk. Its mostly BS about what makes something good, but in the end its all personal choice. If you are like me, and you like a 10 dollar joystick, then hey, who's to say something would be better for you?