Moving vertices around using weights and bones is good. Setting a deform key (meaning moving vertices around by moving each individual vertex) is less good (at runtime, doesn't matter if you export images/video) if your mesh has many vertices, because each key stores the entire mesh (I'm simplifying things a little). Having many deform keys can take up a lot of memory at runtime.
Note that if your mesh doesn't have many vertices and/or you don't set many deform keys, it's OK to use deform keys. For the majority of mesh manipulation, using bone weights is better, both for memory/performance and that it's generally easier for an animator to control.
