: We know that there were trees in Middle-Earth unknown to modern-day shipwrights, eg. Mallorn.

: It is possible that wood with a greater tensile strength than oak was used by the Numenoreans, thus allowing them to build larger, stronger vessels. In this case, the number of refugees could have been more than your estimate. But all very interesting nontheless.

: Does Tolkien mention anywhere exactly what wood was used in the construction of Numenorean ships?

I can't think of an exact description of the wood or woods used in Numenorean shipwrightry but Aldarion and Erendis (Sp?) in U. Tales is probably the best source of such information.
They cetrtainly used wood from Minhiriath around Lond Daer - and from Tolkien's descriptions of the woodlands of other parts of Eriador the species of trees were unexeptional - oak, ash, beech etc. Historically sailing ships were built from a variety of woods (though oak was favoured) pitch-pine was used though it had a short life, and teak (by the British in Bombay); the use of these various woods seems to have had little effect on the size limitations I mentioned. In the Victorian age this size limit was breached for ships of mostly wooden construction though the new methods depended on cross-bracing using iron.

The Numenoreans could have used arcane methods for strengthening their ships, but as the physics of Tolkien's world is generally the same as ours, personally I would doubt this.