What happens if segregated witness never reaches the 95% adoption threshold from miners? Will it still take effect for those transactions where the miners have adopted it?
"This BIP is to be deployed by version-bits BIP9. Exact details TDB."
As soon as testing is complete final details should be determined. It sounds like a segwit soft fork is possible
There will not be a need to wait for a 95% adoption threshold:
"A main benefit of the current Segregated Witness design is that it can be deployed as a soft fork. Once the code is accepted and merged, only miners will need to upgrade; all other users can change their software if and whenever they want to, with no risk of being thrown off the network."
By current agreement Segregated Witness will only activate after it reaches 95% of the miners signaling readiness.
Sending Segregated Witness transactions before that would be foolish, as if they were to be included in a block, anyone would be able to spend the outputs before Segregated Witness is enforced. They are however, non-standard to current versions of Bitcoin Core.
If the 95% threshold is not achieved for an extended period of time, there might be a proposal to lower the threshold.