This is definitely something to watch out for, but in practice (as someone that migrated a system without soft deletes to one that had them) I found that it doesn't tend to come up nearly as much as you might think - usually the table being transitioned to support soft deletes is a relatively core table (since ancillary tables usually aren't worth the complexity to transition) so a lot of your reporting queries will already be pulling in that table. You definitely need to check to make sure you're not missing anything - and sometimes CRUD interfaces will need to be completely revamped to include the table in question - but it's usually not that hard.

You could use a trigger to cascade soft-delete flag toggles, provided all the relevant tables have such a column. Still have to factor that into your other queries, but at least you wouldn't have to make potentially-impossible-to-exhaustively-check joins to figure out if a given row was "deleted".