Hi Philipp,
You may try the cancorr function in the mulSEM package (https://github.com/mikewlcheung/mulsem). It handles missing data with FIML. The details are in Gu, Yung, and Cheung (2019).
Gu, F., Yung, Y.-F., & Cheung, M. W.-L. (2019). Four covariance structure models for canonical correlation analysis: A COSAN modeling approach. Multivariate Behavioral Research, 54(2), 192–223. https://doi.org/10.1080/00273171.2018.1512847
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