It would appear that you are attempting to go about things the wrong way. The "12 word seed mnemonic" system is really designed as a "backup" method to regenerate your wallet should your computer explode or hard disk get wiped etc... you should NOT be entering this every time you are wanting to use your wallet.
Based on your original premise:
Hello,
My goal is to store a few thousands $ worth of BTC as safely as possible as an investment in Bitcoins.
I read the best way is to store them on a USB key, or even better, on a specific device called the Ledger Nano S (less expensive option it seems?).
It would seem that somewhere along the line, you've got a bit confused about software wallets, hardware wallets, wallet files, private keys and seeds.
In my opinion, your best options for long term storage are probably:
1. A "paper wallet":This is literally a piece of paper with the Address/Public Key (in plaintext) and the Private key (possibly encrypted with a password) written/printed on it. You can then give then send bitcoins to the Address, and use a blockchain explorer to view the balance etc. Should you later need to spend the coins, you import or sweep the (decrypted) private key into a software wallet and spend the coins as required (possibly sending whatever the leftover balance is back into a new Paper wallet address)
To enhance security of paper wallets, they should be generated "offline" using methods like rolling dice, or a paper wallet generator on an offline PC using a 'secure' operating system with a Live CD/USB that has not persistent storage or is securely wiped afterwards etc.
The great benefit of a paper wallet, is that it can't be hacked by some guy sitting at a computer thousands of miles away... you can't connect to a piece of paper over the internet!
However, you would need to make sure that this piece of paper is stored securely... taking appropriate precautions against theft (put it in a safe?), fire (fireproof safe?), water (lamination?) etc.
2. A "Hardware wallet":These are usually a small device containing some specific hardware that store and protect your "Seed" and/or generated private keys. Two of the most common/popular hardware wallets are USB based devices like the Ledger Nano S and Trezor.
The theory is that Hardware wallets never expose your seed/private keys to the outside world. They are locked away, encrypted inside the device on special chips or data storage areas... so even when you connect it to your computer/phone, nothing can read the seed/private keys. Instead, what happens is that when you attempt to spend your coins from the associated wallet application, an "unsigned" transaction is sent to the hardware wallet device... the device will then prompt the user for confirmation that they do indeed want to complete this transaction (this is why the devices with displays are popular, as you can see the address and amount that your coins are being sent to, to help prevent being tricked by malware). If the user confirms that the transaction is "OK", the hardware wallet will internally "sign" the transaction... making it valid, and then send just this "signed" transaction back to the wallet application, ready to be broadcast to the Bitcoin network. No "secret" data ever leaves the hardware wallet.
Hardware wallets, generally provide a 24 word seed mnemonic as the backup method. This seed is generated randomly and then displayed during device setup/initialisation and is usually NEVER displayed again. The idea is the user writes these 24 word mnemonic down on a piece of paper and stores it securely like a paper wallet. As explained previously, you can regenerate your entire wallet from that seed should your device get lost.
The advantage of the hardware wallet over paper wallet, is that it is a lot easier to spend from a hardware wallet without compromising the seed/private keys.
3. An "offline" software wallet:Basically, you require two computers. One is used completely "offline". One is used "online".
The "offline" computer, should have NO network connection of any description and is NEVER, EVER connected to any network. You install a software wallet on it... As Danny mentioned, depending on the software wallet chosen, it will either generate a wallet file that needs to be securely backed up (ie. Bitcoin Core) or it will give a seed mnemonic and/or private keys (ie. Electrum). Again, in the case of the wallet giving you a seed mnemonic, like the hardware wallet, this should be written down and stored securely. However, unlike hardware wallets, you can usually get a software wallet to display the seed and/or private keys "at will".
On the "online" computer, you generate a special copy of your wallet from the "offline" machine known as a "watching only" wallet. This has all your addresses/public keys... but contains NO seed and/or private key... so even if someone steals the wallet file, they cannot spend your coins as they do not have the private keys needed to sign transactions. They will however be able to see all your transaction history, coin balances and addresses etc.
To spend coins, you create an "unsigned" transaction on the "online" wallet... then copy that onto a usb stick, transfer it to the "offline" computer... load the transaction into your "offline" wallet, sign it using the private keys creating a "signed" transaction, which you copy back onto the usb stick and transfer to the "online" computer ready for broadcasting to the network.
This might seem VERY similar to the hardware wallet system... and it is essentially the same process, just a bit more complicated and time consuming, not to mention requires a 2nd computer that you don't use for anything other than storing your wallet. Essentially, Hardware wallets have pretty much made the "offline"+"online" wallet system obsolete, but it still does work.
As for which wallet you should use, I think Danny sums it up nicely:
Each wallet comes with its own features and it's own vulnerabilities. You should take the time to understand the wallet that you choose, and then make sure that you secure it so that:
1. You do not lose access to the important information for that wallet.
2. You do not leak the important information to anybody else.
So, before storing a substantial amount of
BTC into any wallet... I'd suggest you take the time to "experiment" with various wallets using small amounts of BTC until you're familiar with the wallets, how they work, how you secure them and how you can safely spend from them.
A small investment of time and a few dollars now, might save you thousands later!