Let's say that I have a mobile application that use pubnub v3 and a web application that use pubnub v7, can these two applications talk to each others (ex: if I send a message from the mobile can the web see it and vice versa)?
All versions of all PubNub SDKs regardless of language can interoperate with each other. Some newer SDKs have more features or may carry more meta-data in the response (subscribe responses, for example) but they are all compatible at a base level.
It's recommended that you keep your SDKs on a version that is no older than 1 year or at the very least avoid using any officially EOL'ed SDK version.