Yes, start migrating the client away from this type of micro-management.
Unless you have a well oiled machine in place to do this type of position checking, there are associated risks. Nothing major but you will get "your" IP banned for short periods if you are not careful. Do it too much, and you may need to use another IP.
I've found that by the time you run the reports which may take over a day or two if you are throttling like you're supposed to do, they are not accurate. Sure, they work as an overall indicator of where you "may be positioned", but that is about it.
I find that viewing the "Search Terms" section of Analytics programs will give you a very good picture of where you stand.
Is rank checking software really needed these days? For those of using WebTrends, are you also using the WPG portion of it?