LinkMan has a limit of number of links because it uses a text database and large text databases are not secure or fast enough for good performance. I don't plan on adding multiple pages to current LinkMan, but I will probably write a MySQL link exchange script sometime in the future.
What you can do is install multiple scripts on your server in separate folders, for example:
http://www.yourdomain.com/links1
http://www.yourdomain.com/links2
http://www.yourdomain.com/links3
etc.
This way you will be able to accept more links and have number of smaller text databases rather than one big one.
Either way, LinkMan is a free script and I haven't found a free one which would do what LinkMan does...
Regards