I'm thinking on installing two WAS cells instead of one cell with two nodes. This way I can better manupulate the application and thus guarantee higher availability.
For an application that is dependent on HTTP access, I realize it would be good to replace the embedded HTTP server (Apache) with an external product. What are some disadvantages, besides the configuration not being central?
WebSphere doesn't embed an Apache-based HTTP server in any meaningful way. Websphere does include a distribution of Apache HTTP Server, called IBM HTTP Server, that you have the option of installing and configuring to act as a reverse proxy to one or more cells. When you pay for WebSphere, you get unlimited support for IBM HTTP Server when they're used together. Notably, SSL is different in IBM HTTP Server.
If you want to use a lot of third-party modules, you might prefer another distribution of Apache, because you cannot recompile or even access the source of IBM HTTP Server. Prior to WebSphere version 9, you might have preferred another distribution because it was based on Apache 2.4. Or maybe you prefer NGINX or squid or using the Layer 7 capability in some appliance.
WebSphere also includes a separately installable component called the "WebSphere WebServer Plug-in" which is a proprietary plugin for several webserver types that provides a consistent reverse proxy implementation running in Apache, IIS, Sun One, etc. The benefits of the WAS Plug-in are primarily that WebSphere itself can generate its configuration file, which is helpful for topologies with lots of servers/clusters/applications or topologies where the servers/clusters/applications are changing frequently.
Another downside to not using the WAS WebServer Plug-in is that the private headers used to describe the client connection are not generated automatically. That is described in this article about nginx:
https://developer.ibm.com/wasdev/docs/nginx-websphere-application-server/