Does MySQL allows incoming queries while altering a table?
During a DDL operation (e.g. alter table) MySQL locks only the objects in question - in this case the table. 

Other tables and databases remain unaffected and new connections are accepted as usual.

On a slave, the DDL operation can't be executed in parallel, so it will delay the replication by whatever time it takes to execute.

The alter operation can increase the general server load CPU/MEM/IO, which can cause it to run out of resources. This rare (with a server with at least a few cores), and pretty much impossible with an empty table, because the alter takes &lt; 1 sec.

The only way a DDL directly affects other connections is if they use the table/s which are modified.