The good thing about anything open source is that it is easy for everything to be replicated and backwards compatibility is hardly an issue. Besides, it is highly unlikely that backwards compatibility would be broken with any well-defined standards. BIP39 is considered a Bitcoin standard and it is likely that it would be supported by wallets far in the future.
I hope so too...
Storing it in anything other than mnemonics is a hassle and highly unnecessary if you're concerned about compatibility; you'll be able to recover them easily even if they are not supported by Electrum in the future.
But, in that case you should know which derivation path the software used in order to recover the address where the funds are located, aren't you?