The tropopl and lenspl functions do take into account the slant paths. This is as opposed to functions like gaspl or rainpl, which are designed for horizontal paths.
Internally both tropopl and lenspl perform refraction in a layered manner as per ITU-R P.676-12. The thickness of the refractive layers increase exponentially from 10 cm near the surface to about 1 km at a height of 100 km. The refractive indices are based either on one of the 6 built-in ITU models (standard, low, mid summer, mid winter, high summer, high winter) or you can import your own measurements.
The losses are calculated based on those refracted paths. Do keep in mind that the lens effect is most prominent at lower elevation angles.