are circular or to be circular
for the sake of simplicity, we have assumed all (the) pneumatic channels are circular/ to be circular.

Question

Answer

for the sake of simplicity, we have assumed all (the) pneumatic channels are circular
for the sake of simplicity, we have assumed all (the) pneumatic channels to be circular 
These are correct
You could also say:
for the sake of simplicity, we have assumed all (the) pneumatic channels are to be circular
if you meant the channels were not yet made and you are stating what shape they should be when they are made

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