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Hexagonal boron nitride (hBN) hosts luminescent defects possessing spin qualities compatible with quantum sensing protocols at room temperature. Vacancies, in particular, are readily obtained via exposure to high-energy ion beams. While the defect creation mechanism via such irradiation is well understood, the occurrence rate of optically active negatively charged vacancies ($V_B^-$) is an open question. In this work, we exploit focused helium ions to systematically generate optically active vacancy defects in hBN flakes at varying density. By comparing the density-dependent spin splitting measured by magnetic resonance to calculations based on a microscopic charge model, in which we introduce a correction term due to a constant background charge, we are able to quantify the number of $V_B^-$ defects generated by the ion irradiation. We find a lower bound for the fraction (0.2%) of all vacancies in the optically active, negatively charged state. Our results provide a protocol for measuring the generation efficiency of $V_B^-$, which is necessary for understanding and optimizing luminescent centers in hBN.