Hard surface modelling with Booleans is a bad idea if you hope to have lightweight, controllable, easy to texture models which may need deformation, transparency, sub surface scattering and the ability to be understood by any other 3d and 2d software.
IConnecting curved surfaces like two cylinders is best done as a subdivision surface modelling task
The shrinkwrap modifier is your best bet for a good topology.
It takes ages to make these!! Please consider supporting me!