What happens to my wallet when I only
1000 accounts with
0.0001 ether and the
tx-fee is about the same, I can't spend anything anymore?
Correct. You need to pay transaction fee for each transaction and one transaction can only tranfer assets from one account. Or if the origin account is actually a smart contract then it can transfer to multiple accounts in the same transaction.
Ethereum is not meant for such use - if you need similar (UTXO) functionality you should write a smart contract for handling the assets. Then you simply sends all the assets to the contract and the contract keeps some sort of track of the assets' origins.