Hi Yanis,
I don't have experience with Matisse so I'm not sure I understood whether your 200 000 points are considered during the meshing process? If so, I could understand why that computation is difficult.
I know we have worked with that many points in BlueKenue and have not had any problems. The work method we use is similar to that described by Christophe. We first generate a flat mesh (0 elevation) with constraint lines, boundaries, density zones and some hard points. We then interpolate our topo, bathy on that mesh with BK. I think the largest mesh we have generated so far is around 600 000 nodes. The largest .xyz file interpolated so far was several million points.
If your are interested to try, there is one other thread on assigning bathymetry with BlueKenue ->
Telemac Forum : Assigning bathy. Sebastien put some links to the BK documentation. As far as I know, if you have a working flat mesh, you have a lot of software choice to interpolate bathymetry onto it afterwards (Fudaa, Telemac, BlueKenue, etc)
Hope this helps,
j