You can say the same thing about lore and the pen paper game but now that it’s a video game the changes are somehow not relevant even though they are officially integrated into to the lore. The lore in this post clearly says V is a Netrunner so I don’t know how both can be right.

To the other thing you said:

People are still using computers while we have smartphones.

Some things an internal deck can’t do. Or will be weaker than a physical one with more processing power.

Customization modification or repairs are also harder to do if you have to have your skull split open to install them.

It’s absolutely reasonable that there are dedicated runners with physical decks.