Data-driven materials design often encounters challenges where systems require or possess qualitative (categorical) information. Metal-organic frameworks (MOFs) are an example of such material systems. The representation of MOFs through different building blocks makes it a challenge for designers to incorporate qualitative information into design optimization. Furthermore, the large number of potential building blocks leads to a combinatorial challenge, with millions of possible MOFs that could be explored through time consuming physics-based approaches. In this work, we integrated Latent Variable Gaussian Process (LVGP) and Multi-Objective Batch-Bayesian Optimization (MOBBO) to identify top-performing MOFs adaptively, autonomously, and efficiently without any human intervention. Our approach provides three main advantages: (i) no specific physical descriptors are required and only building blocks that construct the MOFs are used in global optimization through qualitative representations, (ii) the method is application and property independent, and (iii) the latent variable approach provides an interpretable model of qualitative building blocks with physical justification. To demonstrate the effectiveness of our method, we considered a design space with more than 47,000 MOF candidates. By searching only ~1% of the design space, LVGP-MOBBO was able to identify all MOFs on the Pareto front and more than 97% of the 50 top-performing designs for the CO$_2$ working capacity and CO$_2$/N$_2$ selectivity properties. Finally, we compared our approach with the Random Forest algorithm and demonstrated its efficiency, interpretability, and robustness.