One approach is to use a replacement rule for the result, something like this:
In[1] {1, na, 3, na, 5} - {1, 2, 3, 4, 5}
Out[1] {0, -2 + na, 0, -4 + na, 0}
In[2] {1, na, 3, na, 5} - {1, 2, 3, 4, 5}/. x_ + na -> na
Out[2] {0, na, 0, na, 0}
Another approach would be to define UpValuefor naso that addition (and subtraction) with it has always led to na; eg:
In[3] na /: Plus[___, na, ___] := na
UpValues , , .