Gumby
The lowering link is not going to have a major effect on the performance of the shock absorber. But the effect is none the less detremental. When you lower a bike you need to reduce the travel of the shock as well, other wise the wheel will contact the underside of the guard. The lowering link also affects the progression of the shock reducing is ability to firm up as it goes through the stroke. The best way to reduce the travel at the rear is to have a tuner reduce the travel within the shock by placing an internal spacer between the sealhead and the top out plate. This reduces the travel and slows the momentum within the shock by altering the starting point in its progressive curve. This should not present a problem to any tuner and I would not expect to pay a huge amount of money. Plus you get the added benefit of having your shock serviced at the same time.
Regards
Terry Hay