I was preparing to create an update site for my custom nodes when I came across an item in the product matrix called "Custom node repository". We have the KNIME server, and I was wondering what the item in the product matrix refers to... will it help me deploy my custom nodes within my company?
No, this is for creating your custom structure in the node repository (e.g. hiding nodes, creating new categories, etc.). Your nodes can easily be distributed by an internal update site. The Eclipse documentation explains in detail how to create an update site.