At Yahoo we drop columns from the previous version the next time we upgrade the database, e.g. if you stopped using a 1.0 column in version 1.1, then you drop that column as part of the upgrade going to 1.2. The key thing is always being able to roll back if things go seriously wrong; hardware is much, much cheaper than downtime.
Unless you really need the space, I suggest leaving the columns there. Fewer chances for error. If your columns are nullable, the amount of space taken up by an obsolete column tends to one byte, particularly if old data is deleted.
If it's just 1 column, and it doesn't store much data, then probably no.
If it's a bunch of columns and it's taking up lots of disk, they they probably migrate what they need to a new table and drop the old one. Altering tables is usually not a good idea. In mysql it can stop replication and can mean hours or days of downtime depending on the situation and amount of data.
In practical terms you generally don't tho'. You might need them again, for example, for some as-yet-unplanned new feature. And doing so is of limited value anyway in many databases, you won't get the space back without a re-org and that's a costly operation to do hot, if you even can at all.
