What if those 2 addresses have 1000+ transactions in history, would it be affecting the loading again on new wallet?
Possibly, but only on the first sync... and the first time you try to consolidate or spend the UTXOs (or if they build up a large number of UTXOs again from 1000s of pool payouts). Consolidate regularly if you can, and it should stop it becoming a problem.A new SEED is not imperative thing. One can use the old one but define the new derivation path. For example, if the old derivation path for the pool with the native segwit addresses was like this m/84'/0'/0' one can outline the next pools with the derivation paths like m/84'/0'/1' , m/84'/0'/2', m/84'/0'/3', .... and so on.
Yes you can... but then you also run into the problem of needing to ensure you keep good notes regarding what you have done... otherwise, you will run into problems trying to restore the wallet in the future as most people don't (and some wallets don't allow to) modify derivation paths...Both options are valid, but I would say that having a new seed with a default derivation path is probably less hassle in the long run. User preference I guess...
Agree, everyone should (even must) keep all out good record of all stuff that allow to reach (without snags) the relevant addresses. Keeping records with identical SEED (say the same 24 words) but with different derivation paths is much easier than with distinct SEED. Eventually, unchangeable SEED can be memorized what is impossible to do for the SEED bundle. As to "some wallets don't allow to" change default derivation path - we speak of Electrum, right, and it is capable of that. I'm doing it right this way - constant SEED + different derivation paths. The latter is very easy to memorize - increase the last index by 1 and you are sitting pretty.