We investigate new approaches to the deuteration of C3H2, HC3N and HC5N in dark clouds, following the suggestion that protonated HC3N might form different isomers, a linear structure (HC3NH+) being the most stable. We consider the effect of linear HC3NH+ and HC5NH+ on the formation of HC3N and HC5N, and find that deuteration ratios at approximately 10 K are reduced, in the case of HC3N to values significantly below those observed, such that a deuteration mechanism other than direct deuteron transfer is probably required for cold clouds. However, C3H2 has the highest observed deuteration ratio in cold clouds (greater than or similar to 10 per cent), several times larger than can be accounted for in existing models. Various potential solutions to this discrepancy are tested, the most promising possibility being that the presumed precursor ion C3H3+ is directly deuterated by reaction with HD molecules. With the addition of this assumption to the above model, we predict deuteration ratios for both C3H2 and HC3N which are close to those observed, since their formation mechanisms are closely linked. Moreover, this is achieved without seriously affecting other observed species with well-explained deuteration ratios. We also investigate the effect of the possible neutral-radical formation of cyanopolyynes, and find that their deuteration ratios are reasonably close to observations, although the absolute abundances of the undeuterated forms may be unrealistically high. In addition, we present graphs of predicted deuteration ratios of var-ious species