Hydrofoils are now widely used to reduce hydrodynamic resistance, leading to increased velocities and sailing crafts performance. However, designing hydrofoils for sailing vessels such as windfoils and kitefoils remains a complex challenge, as the ride height plays a critical part on the stability and performance of foiling vessels. Furthermore, the strut between the board and the plane-like foil (called the shaft) is highly loaded and subject to significant deformation, leading to potentially important Fluid-Structure Interaction (FSI) effects. Consequently, it is now critical to consider the ride height and the FSI effects in Velocity Prediction Programs (VPP). This work first presents the development of a novel five degree-of-freedom (DoF) Velocity Prediction Program (VPP) for foiling crafts, which includes the FSI effects on the shaft of the vessel. Hydrodynamic forces are computed using a vortex lattice model with a viscous correction, solved by the panel method implemented in the software Athena Vortex Lattice (AVL). The structural behavior of the shaft is introduced in the VPP in the form of an analytical model derived from experimental tests on real shafts. This improved VPP is then applied to a generic plane-like hydrofoil, typical of a windfoil sailing upwind at a speed of 9m/s (18kts) and approximately a 20° windward-heel. Twenty shafts of different stiffness are tested, and their respective deflections, as well as the equilibrium state computed by the VPP, are compared. Results show that for a static analysis the equilibrium state and the performance are barely affected by the stiffness of the shaft. However, the use of a flexible shaft leads to a different distribution of the lateral hydrodynamic force (anti-drift) onto the different parts of the foil.