I draw a separate way for the towpath. Your point regarding the aqueduct is quite valid and unfortunately there is no way of modelling this properly at the moment.
Unlike highways where there is an assumption that foot traffic also has a right of way, canals often run through private land where there is no right of way. The towpath key certainly could model the existence of a towpath but there are problems with it. Which side of the canal is the towpath? What about where there are towpaths on both sides of the canal? What about the access rights?
Drawing it as a way allows you to solve these problems simply. The aqueduct issue is problematic but ultimately could be solved with relations linking the towpath way to the waterway.