If you mean classic DW, I doubt they catered for commercial breaks at all. If you mean other shows, such as TNG, that aired first on channels with commercials, yes, the breaks are a lot more obvious. I expect the script has to be written with pacing that takes breaks into consideration. However, I have no knowledge of how production deals with such things. When I watched shows in the US, the placing of commercial breaks often seemed quite random and disruptive.
I meant in general, not Doctor Who.