Thank you for all your answers. What I did is come back to the original path and modify the config file to make it working. Now wallets are loaded with the flag -walletdir=.../testnet3/wallets.
I still don't know why it doesn't work before but now it works. I'm still strugling with bitcoin-cli because he doesn't want to read config file in PATH. Rather than bitcoind is running correctly into this path...
I hope to find the problem soon. Thanks again everyone for your answer.
Maybe because you used -datadir=.../Bitcoin/testnet3 instead of just used -datadir=.../Bitcoin and because in both directories /Bitcoin/testnet3 and /Bitcoin/testnet3/testnet3 have the same wallets folder, then there is a possibility that a conflict have occur when the client reads the wallet file.
Have you ever tried running bitcoind testnet using datadir=.../Bitcoin instead and using the same bitcoin.conf file used by the Mainnet. I guess it will work out as you want (running normally as when you run the Mainnet).