Siphoning method is better because it collects all the faeces, even small partials. Depending on the volume of water and surface area of tank select diameter of siphon pipe. Pipette method may not collect all the faeces.
I am not sure what you meant by the 'field'? To determine digestibility there is '1 must' the feces must be collected as soon as possible without breaking them. Siphon is convenient but will break feces. If you can design a conical tank which contains feces at the bottom or a plankton net covering the small cage, you can collect feces without using siphon or pipette. .
Using siphon is an applied method for feces collection but in this method the risk of mixing feces samples with food particles is probable which can affect the accuracy of measured parameter .So pipet collecting method is more accurate.