When he chose to, it was on purpose. He was wholly capable of writing clearly. Nesting levels of meta-text, intentionally adopting a different authorial voice as a metatextual gambit, etc. were all pretty new things when he was alive.
They're trite or annoying now, but it's still important to know that he wasn't just being a whiny prat. They're signs that maybe you should or should not take this or that particular penname totally seriously. ('johannes silentio' was super prolix, etc. )
Read Soren K. when he was writing with his own name. I taught the Philosophy class on Kierkegaard every semester, because our Philosophy Chair hated him so much. We ended up being good friends and he now actually enjoys S.K. now.
S.K. is the most influential and impacting philosopher of the 20th Century (Arguably but I'm pretty sure I'm right). You might not like what you know of him but he took over almost all the theological/philosophy thought by storm 50 years after his death. Heck there were no English translations till the 1940s. He went from a forgotten Danish philosopher to the founder of Existentialism. Hegel never even knew he was alive let alone read his rebuke to his system of philosophy, but S.K. surpassed all of his contemporaries.