Yes and no. Sometimes a manufacturer will offer two size variations of the same value caps. Panasonic, for instance has the THA can-type caps that come in "tall skinny" and "fat short" for the same values.
To an extent, yes, its good to increase the size of these. But you need to be careful as well because increasing too much will create too much inrush current and could burn out other components, diodes, rectifiers, etc.
Since capacitors have a pretty relaxed tolerance anyhow (+/- 20% usually) It's not a bad thing to bump that up a bit more, say, 30-40% for the power supply ripple filter caps or capacitor-coupled output caps.