Considering they operated in France and the Netherlands and even 'had a shop there' (whatever that means): Yes, but looking at all the articles I'm pretty sure they are also building a case against EncroChat for participating or actively facilitating criminal behavior, in which case the point is mute anyway.
Some requests can be made to ask you participate making you sort-of free of prosecution as you are cooperating, but I doubt they would do that with companies with shady structures and owners.
EncroChat is not an app you get from an app store. It came with the EncroPhone, which are physical Androids you rent for some absurdly high price (like $3000/year-ish). And EncroPhone didn't sell online. You had to get them via a reseller i.e. someone you knew, or they had a few physical stores in the Netherlands.
Are they supposed to simply accept that the government will hack into their servers and users devices with no compensation?