Sounds like you never really understood Notes.
For example, it's really hard getting sales people to keep corporate contact information up-to-date once they've started keeping their contact info in Notes. It's easy for them, they can replicate to their desktop and access the info while they're on the road. It's free form, so they can add comments. Great for sales-people. Sucks for billing when the client has moved and the sales guy who knows about it can't be bothered to update the "real" client database.
Our clients find it really easy. An example (with names changed to protect innocent!):
An international company has our bespoke CRM system built in Notes deployed in 25 countries over all 6 continents. In each the salesman can update the company name/address on his local replica on his local laptop. When he replicates the database the change gets pushed up on to the server. Each night the nightly integration with their backend AS/400 pushes the change back to their ERP system, where the billing is done.
In your example your problem was not that the salesmen had a separate clients database. It was having a clients database the salesmen couldn't use the way they needed to, so they had to build another one in Notes.
Notes is great a solving business problems in a quick and cost-efficient manner. There is nothing like the wow factor of talking to a user in the morning, and showing him a fairly functional prototype in the afternoon.
Don't get me wrong - Notes/Domino sucks at many things, but as long as you don't ever treat it like a relational database things work fine.
To truly get the power of Notes, you have to integrate it with the core systems. Or (where it is sensible) run your core systems on Notes.