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You can't highlight PDFs in iBooks, but as mentioned there are many other apps that will allow you do do that. Also as mentioned, pdf is not a very good format and the screen size of an iPad mini may be a bit small, depending on the original page size of the files you're going to read.
Whatever app you use, you won't be able to change the text. The app will only add the highlights and notes in a layer on top of the existing content. But as meera says, you can always make a copy of the book if you're worried.
Personally I find Goodreader slow and clunky, although it's very rich in functionalities. iBooks is good if you just want to read, but again you won't be able to highlight or annotate.
I use MarginNote for all my non fiction reading. You can highlight and annotate PDF and ePub books and save your notes to Evernote. The app can be slow and frustrating sometimes but I like it.
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