No it's not. I fly regularly intra-EU and maybe once (?) have had to take my shoes off in the last 5+yrs....can't even remember. I don't know which airports you transit/use but I go throw most of the major ones across EU pretty regularly.
All major ones.
Usually I see it happening to those lucky ones carrying boots or shoes with thick sole.
Maybe I haven't been paying that much attention. I travel wearing a mix of dress/ converse/ boots type shoes but no issues so far. Neither has my GF had any issues (that I know of).
Naturally it is all anecdote data, I am not asserting that it is always like that.
Not my experience, at least flying from PT to ES, CH, DE.