Well, the AccessPoint does a couple things when you first open it: (1) tries to find out who you are (authentication), and (2) populates a list of documents that you have access to (authorization). Or, rather, QlikView server performs point #2, but the QVWS/IIS needs to communicate with the QVS to display the list to you, the user.
The volume of QVWs goes to point #2, as does the relative location of the applications, and of the servers. Meaning, if your QVWs are hosted on network storage (NAS1) and your QVS is on one server (Server1) and your QVWS is on another server (Server2), those are all nodes that must be navigated by the network before your AP will display the list of application to you. Make sure that the network speed between all components is good.
Point #1 has to do with the directory against which you are authenticating, and the QlikView Service responsible for it (the Directory Service Connector, or DSC). It is always a best practice to keep the DSC on all machines that need. For example, if you have a Publisher box and a Web Server box, make sure that each one has a local DSC, and that you're not trying to use the DSC from one machine across the network (doing so adds unnecessary overhead). In addition, The DSC needs to be able to communicate with your directory (Active Directory, for example) to authenticate the username. Check with your network admins to make sure the ports between the web server box and the Domain Controller are opened properly. I've personally seen AccessPoints take over a minute to load because of this issue.
Hope this helps.