Yes. There is a hard limit of 100 runes per trade or bid. If you wish to add any more than this, you will need to split it up into multiple trades/bids.
A rune is immediately locked as it is added to a trade or bid. This means it may no longer be upgraded, activated, sacrificed, or added to other trades or bids. Finally, it is removed from all current decks.
A trade owner has up to 24 hours following the end of his or her trade to make a decision. Expired trades may be accessed through the "My Bids" page. After 24 hours, the trade is automatically canceled by the system.
Once a trade is canceled (either by the trade owner or the system after a trade has expired), all credits and runes are immediately unlocked and returned to their respective owners.
The answer is yes. The champion is traded as-is and absolutely nothing about it will change when traded. This is done purposely. Also, be on the lookout for higher profile trades that commonly include these as part of the deal.