As long as there is a reasonable amount of soldermask between the pad and the via hole, you won't have issues with solder wicking into the via, which is typically the main concern with via-in-pad. Make sure that you have enough soldermask so that the soldermask width minus your PCB shop's soldermask tolerance is sufficient to guarantee a strip of soldermask.
However, as others have pointed out, you may have issues with acid traps or uneven heating. For a one-off, these are likely a non-issue, but for a product, these should be taken care of. Because it's an LED (and therefore shouldn't be drawing too much current), use the smallest via and annular ring your boardhouse allows, and see if that works. If that fails, two vias on either side, overlapping the pads but with soldermask in between pad and via should be reasonable. However, if you are under such tight size constraints that this is necessary, consider opting for filled via-in-pad, and then you can put vias wherever you like. Sort of.