Wow! I've never noticed to it! it's a bit hard to explain, Anyway:
Yes, Despite there is a very subtle difference between وقت داشتن and وقت کردن, you can use them interchangeably and you can also use رسیدن for a same situation which has a same meaning as وقت کردن . Here are some examples:
If you had time wash the dishes please.
اگر وقت کردی، لطفا ظرف ها را بشور
اگر رسیدی لطفا ظرف ها رو بشور
اگر وقت داشتی لطفا ظرف ها را بشوی
As you can see in the first two sentences I used the verb بشور which is the informal way of saying بشوی. I wrote it in purpose to show you وقت کردن and رسیدن are used in spoken language. I can say I've never seen them to be used as a formal verb in the books.
About that subtle difference I can say وقت کردن is for what you did in past and will do in future, not present.
When you say: الان وقت دارم که این کار را انجام بدهم means I've got time now for doing this.
But when you say: وقت می کنم این کار رو نجام بدم the listener finds out that even though you're busy but you will have time for doing this.
وقت کردم به گل ها آب بدم it means I had time to water the flowers and I actually did this.
But وقت داشتم به گل ها آب بدهم means I had time to water the flowers but it's not clear if I did this or not.
your sentence: برای خواندن همه این کتاب ها وقت ندارم means you don't have time to read all these books but I can't be sure that you won't read them. But when you say وقت نمی کنم این همه کتاب رو بخونم I can understand that you don't have time for it and you won't do it.
I hope that after reading this explanation you are not confused now! :p