Even if you travel a long distance, the risk of developing a blood clot is generally very small. Your level of risk depends on the duration of travel as well as whether you have any other risks for blood clots.
There are a few reasons why our bodies might ache after flying. First, we are prone to dehydration when we fly because the air in aeroplanes is very dry. This can cause our muscles and joints to ache. Second, the change in air pressure when we fly can also cause our muscles and joints to ache.