Here is what I have found so far in relation to multiple keys with JTable in Joomla 3.4
Looks like since platform 11.1 there is some support for multiple primary keys in JTable.
JTable::getKeyName(true) will return an array of primary keys for a table.
JTable::load() this abstract class possibly accepts an array of primary keys (array of fields to match), Loading a row from the database and binds the fields to the object properties.
Since platform 12.3
JTable::getPrimaryKey($keys) accepts an array of primary keys, returning an array of primary key names and values.
JTable::appendPrimaryKeys() seems to address multiple primary keys