Problem: SRTM ocean depth is 0 meters, however this is not water in arma3, how can I make my ocean deeper?

Well you can use create/flatten terrain feature in global mapper.

Use like openstreetmap or world street map as your guide where the ocean is. Now create area feature (draw shape, ie polygon) for your ocean.

This does not have to be very accurate because we have to do some cleanup in L3DT (or buldozer?) anyways, of course its less work in there the more accurate you draw this area feature.

It might be good idea to save it as new layer to keep things organized.

Select your new ocean layer, RMB → edit - edit area feature. In feature attributes box click Add button, give attribute name “elevation” and value “-50”, click OK and click OK.

Again with new ocean layer selected click RMB → advanced feature creation options → terrain - create/flatten terrain from selected area(s).

Now you see elevation grid creation options dialog. First lets call this layer like “flattened_ocean_to_-50m” so type that into the description edit box.

On grid spacing box tick “manually specify the grid spacing to use” and give some small value, no idea if its worth to put lower than your terrains cell size in meters, but it seems to accept and do good work like with value 10. Then just click OK to have it calculate, when its done you should end up with blue color inside the ocean shape and if you hover mouse over it status bar shows -50 m as height (elevation).

Have SRTM online source loaded with “flattened_ocean_to_-50m” layer as well as your regular user created feature grid box (remember to select user created feature grid), then just export SRTM online source normally as ASCII heightmap and it will be modified for -50m ocean depths.