Answer
Yes, this is the expected behavior. Each Routing Engine runs its own SNMP process (snmpd), allowing each Routing Engine to maintain its own engine boots.
However, if both routing engines have the same engine ID and the routing engine with lesser snmpEngineBoots value is selected as the master routing engine during the switchover process, the snmpEngineBoots value of the master routing engine is synchronized with the snmpEngineBoots value of the other routing engine.
For more information, click Understanding SNMP implementation in Junos OS.