The blocks in older chain are deactivated for those in the newest chain.
This is not always the case, because the total chainwork is counted, the block time can be older, but it has to meet the consensus.
What if the nodes receive blocks shorter than the active chain, does chain organisation also occurs?
It depends on chainwork.
Does this mean only the transaction present in the longest chain remain valid after reorganisation?
Yes, in the heaviest chain, not the longest, Satoshi changed it from "the longest" to "the heaviest" by adding code for checking Proof of Work for that reorged chain.
What happens to the transaction in deactivated blocks?
It does not exist, unless it is also included in the heaviest chain. You can use your CPU and mine today a new block, on top of the Genesis Block, and pretend it happened in 2009. And guess what: those coins will never exist, so you will not get 50 BTC for doing that. This case is the same for any transaction, coinbase or not.