Glenn:
1. In September, 1940 Austria (which the Danube runs through - hence "Die Blau Donau Waltz") is PART of Germany so Danube traffic serves that part of Germany. Likewise the Danube services parts of Czechoslovakia, and the industries of this "protectorate" are vital.
2. In September, 1940 Hungary and Romania, while friendly to Germany are NEUTRAL powers, as is Yugoslavia which is more on the fence. In any case, the Danube shipping is essential for these countries and a significant proportion of the barge traffic is on vessels owned/controlled by these countries. Are you suggesting that Germany seize these barges from neutral countries? This would piss them off and hurt their economies and they would resist this. Don't forget that Germany gets a huge percentage of oil from Romania, and it has to pass through Hungary to get to Germany (Polish rail lines can't handle much extra traffic. Some may come on barges owned by Romania up the Rhine.
3. Connections between the Danube and the main German river systems are limited in 1940, and some barges simply won't fit in those locks.
Bottom line is that while you MAY get some barges from the Danube system, the overwhelming majority of losses will need to be BUILT. To the extent that barge traffic on the Danube is reduced by this, industries in Austria and Czechoslovakia will be impacted. If you attempt to seize neutral shipping, especially after SEALION v1.0 flops, forget making allies/co-belligerents of these countries.