I owe to my years of training in ashtanga vinyasa the habit to count my breath in asana practice. Viniyasa in, five breaths, vinyasa out, next posture...
This habit has one great benefit: it focuses the mind on the breath. In a way, you could say that you are doing a somewhat contorted form of Anapasati practice, and it's actually a lot easier to focus on the breath this way than when you are just sitting there, doing nothing.
But it is also a very mixed blessing because counting means that you are focusing primarily on quantity, and, well, yes, anyone who's walked into a hard core ashtanga class knows that quality can suffer, or even be ignored all together, as a result.
Recently, I started questioning my counting habit. These days, I tend to hold postures for a lot longer than five breath anyway, and to come out when my body's telling me to, rather than after a fixed number of breath. So while for asymmetrical postures such as twists, counting still helps to ensure I'm holding the posture for roughly the same length on both sides, for symmetrical postures, counting was often a distraction rather than a help. When I started to drop counting all together, I could start to focus more on the quality and the length of the breath, which generally resulted in a softer and more subtle practice.
In pranayama practice, counting, while also very useful, can have pernicious effects too. Not only it focuses the mind on quantity rather than quality, but it can easily pull it into a competitive mood where we try to do more and more (for example with longer and longer kumbaka), and forget to notice when we are doing to much. Again, experimenting with dropping the counting all together was very interesting, and I now tend to use only occasional counting, more as a way to check where I am rather than as a guide to where I should be.
In Anapasati (mindfulness of breathing meditation) practice, counting can be useful too. The advice that is generally given is to count to a fixed number of breaths, usually between 5 and 10, up, then down, then back up again, on and on. If the mind is distracted or unsettled, this can be useful in keeping it a little more steady by giving the right brain something to busy itself with, but, here again, counting can quickly become a prop.
Ultimately, counting is a tool. And, as anyone who has used a sledge hammer to crack a nut can tell you, using the right tool for the job at hand makes the job easier, safer and quicker.
So, still counting? Well, sometimes...