I'm not sure exactly Daniel, since I haven't tried smugglers 3 with Nvda.
I do know it uses far more standard windows controls than 4 or 5, list boxes, buttons etc, so sometimes you might be best off turning off screen review and using arrows, eg, when looking at lists of upgrades or the holds of your ships.
I do remember needing to actually use simulated mouse clicks far more in the game than in 4 or 5, eg, I'd have to press the space bar twice in rapid succession to perform a double click on items with Supernova, rather than having supernova's usual instant double click keys work, so you might give that a try (I the left click emulation in Nvda is numbpad plus but don't quote me as I haven't had to use it thus far).
In general however I would recommend playing smugglers 5 over 3, , particularly because the interface less haphazard and you can find a guide about s5 and Nvda in the articles room.
Even in gameplay terms though, while 4 didn't replicate everything from 3, 5 now sort of does. orbital turrits and a lot of the ships are back, plus 5 advantages such as far more interesting combat, actual stories for each planet, professions, npcs etc, (you can even now still get married).
3 is a great game and I don't regret the time I spent with it, there is a reason it's now essentially been down graded to a freebee.
With our dreaming and singing, Ceaseless and sorrowless we! The glory about us clinging Of the glorious futures we see,
Our souls with high music ringing; O men! It must ever be
That we dwell in our dreaming and singing, A little apart from ye. (Arthur O'Shaughnessy 1873.)