i always thought that the tubes were more or less a "representation" of underground tunnels but due to game limitations or perhaps by design, only the very top of the tube sticking out from under the surface is shown. tubes can be driven over so having windows sort of defeats that ability.
if you want to get really specific about it, if tubes had windows they would now be vulnerable to blight. if tubes have windows they now need seals around the windows which are exposed to the surface. blight gets in, spreads thru the tubes to the structures and youre dead.
my main point was the first. we arent even living on other planets and yet even WE (at this point in history) know that the safest way to get from place to place on a hostile world is through the use of underground, concrete tunnels. the colonists in op2 would of course know this and building a tube with the top sticking out is just as difficult as burying the whole thing so it cant be ruled out as 'more efficient'. we see tubes on the surface because it was easier than having an underground view that had to be switched on. i havent played op1 but isnt their tube system like this? anyway, i consider underground tubes canon and their surface visibility merely an aid for players. tubes having windows doesnt work because tubes arent 'really' on the surface and they would only provide another system to fail or be exploited.