Hello Karine,
TELEMAC-2D and TELEMAC-3D have to work in plane projection like UTM, Mercator, Lambert.
If using SPHERICAL COORDINATES = YES and geometry files in longitude/latitude, the first thing done is to convert the coordinates in Mercator. From that step to the writing of results, everything is done in plane projections, that is why if you want to add drogues, you have to give their coordinates in Mercator projection. You can read the formula used for conversion in $HOMETEL/sources/utils/bief/read_mesh_coord.f subroutine.
FYI if using SPHERICAL COORDINATES = YES and tidal database like TPXO, you have to set GEOGRAPHIC SYSTEM = 5 as when every interpolation with tide is to be done in Mercator projection at that step (done after the 1st conversion explained at the beginning). Anyway, if not set to 5, it is automatically done with a warning message.
Hope this helps,
Chi-Tuan