Do regular ALTERs weaken the performance?
It's an intuitively-sensible concern that you've raised because it would seem to make sense that frequent DDL operations might leave little bits of messiness behind, but my experience has been that this concern is unfounded with InnoDB.

Prior to MySQL 5.6, the vast majority of ALTER TABLE operations actually rebuild the entire table with the new structure, copy all the data, then swap in the new table and delete the old one... so, I see very little potential for frequent changes to have a negative impact down the road.

You might, though, be well-advised to OPTIMIZE TABLE on tables where you've repeatedly inserted and deleted test data to clean up wasted disk space and rebuild the indexes, but unless your test data has been comparable in size to your production data, even this will disappear in the mix as the tables take on live data.