Umm, it absolutely has an effect. Starting with the sound card, if you are using an analog output, then yes, the sound card will have an effect on quality, since it has to convert the digital sound into analog.
The receiver has the most effect on sound, since it is what's processing and amplifying the sound. A 15 dollar boombox will not have the same sound as a thousand dollar receiver.
The speakers also will obviously have an effect, especially with shelf systems like you have. Most manufacturers ship very cheap speakers with those systems. And most home theatres in a box (all in one) will have the same problem.