In this paper, we explore the issue of inconsistency handling over prioritized knowledge bases (KBs), which consist of an ontology, a set of facts, and a priority relation between conflicting facts. In the database setting, a closely related scenario has been studied and led to the definition of three different notions of optimal repairs (global, Pareto, and completion) of a prioritized inconsistent database. After transferring the notions of globally-, Pareto- and completion-optimal repairs to our setting, we study the data complexity of the core reasoning tasks: query entailment under inconsistency-tolerant semantics based upon optimal repairs, existence of a unique optimal repair, and enumeration of all optimal repairs. Our results provide a nearly complete picture of the data complexity of these tasks for ontologies formulated in common DL-Lite dialects. The second contribution of our work is to clarify the relationship between optimal repairs and different notions of extensions for (set-based) argumentation frameworks. Among our results, we show that Pareto-optimal repairs correspond precisely to stable extensions (and often also to preferred extensions), and we propose a novel semantics for prioritized KBs which is inspired by grounded extensions and enjoys favourable computational properties. Our study also yields some results of independent interest concerning preference-based argumentation frameworks.