Virtual pruning of simulated fruit tree models is a useful functionality provided by software tools for computer-aided horticultural education and research. It also enables algorithmic pruning optimization with respect to a set of quantitative objectives, which is important for analytical purposes and potential applications in automated pruning. However, the existing studies in pruning optimization focus on a single type of objective, such as light distribution within the crown. In this paper, we propose the use of heterogeneous objectives for discrete multi-objective optimization of simulated tree pruning. In particular, the average light intake, crown shape, and tree balance are used to observe the emergence of different pruning patterns in the non-dominated solution sets. We also propose the use of independent constraint objectives as a new mechanism to confine overfitting of solutions to individual pruning criteria. Finally, we perform the comparison of NSGA-II, SPEA2, and MOEA/D-EAM on this task. The results demonstrate that SPEA2 and MOEA/D-EAM, which use external solution archives, can produce better sets of non-dominated solutions than NSGA-II.