Both are a bit dated and need replacement (we are working on it), but they are perfectly fine (if used correctly).

StatNonParamTestPDM is a simpler test, where one assumes the two groups to be perfectly matched as one cannot control for co-variates such as age, gender etc. If you have a simple 2 group setting where a test like student t-test would be appropriate, then that setting is right for StatNonParamTestPDM. 

shapeAnalysisMANCOVA is more advanced and can handle multiple co-variates and do both group tests as well as interaction tests. It can be a bit cumbersome to handle and has a bit of a learning curve, but it should give you a powerful testing tool.