Here is my view.
If this might help, I've been learning Arabic for 8 years and I can say now, I can really defend myself in the language. However, my experience is that: yes, it's like this. In daily writting language, vowels just disappear, but at the end, this is not a big deal since you're going to take it as normal. For those, words you already know, it'll become like intuitive and for those other you don't know, mostly, for its lexical constrution you'll know how to pronounce it. It's a matter of time :-)
Anyways, Arabs, depending on which region they come from, they pronounce words differently.
You know... Arabic language, at the same time it's beautiful, it's also amazingly rich in lexic.