Use vias or point to point connections?
A via creates a routing block on all layers.1 This can come back to bite you later, when you're trying to complete the final connections, especially if your board is tightly packed.
A surface track also creates a routing block on one layer, and the outer layers are a particularly critical resource in SMT designs.
My normal approach is to start by placing the extra via, but then replace it with a surface trace if possible during the final cleanup passes toward the end of the editing process. Or sooner, if I get to a point where it becomes obvious that I won't be needing to route anything between the two components.

1 Blind vias block fewer layers, but add significant cost to the board.