Bill,

Other than the cost considerations, there really isn't a lot of risk involved.  That is, if you fill and cap the vias (like IPC 4761, type VII).  Once you do that, the pads are simply pads, the vias are simply vias - with big pads on the top and bottom.  The risk is more a factor of the quality of Fab vendor you use, but that goes for pretty much every feature on the board.

If you have the room to route the board without vias in pad, there's no reason to use them.  But if you need them, there's little reason NOT to.  You might spend more on a larger enclosure and larger board than you do on filling and capping vias..

Pete

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