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The short answer is no. Only 1 thermostat per zone. I can see 2 options in the control of these 2 systems. One is that you can prioritize operation of equipment as shown below, and two is that you can use EMS given the available actuators. I am not sure from your description if you want the ideal loads system to run all the time or just when the zone load is not met. When you say " second one is an ZoneHVAC:IdealLoadsAirSystem. Its job is to supply air into the zone with given temperature, humidity ratio and massflow specified by an EMS program", it sounds as if you want the ideal loads system to run all the time. In that case you would make that system priority 1 in the list below.

ZoneHVAC:EquipmentList,
  ZONE 1 EQUIPMENT,        !- Name
  ZoneHVAC:Baseboard:RadiantConvective:Water,
  ZONE 1 Baseboards,      !- Zone Equipment 1 Name
  1,                       !- Zone Equipment 1 Cooling Sequence
  1,                       !- Zone Equipment 1 Heating or No-Load Sequence
  ZoneHVAC:IdealLoadsAirSystem,  !- Zone Equipment 1 Object Type
  ZONE 1 Ideal Loads,      !- Zone Equipment 1 Name
  2,                       !- Zone Equipment 1 Cooling Sequence
  2;                       !- Zone Equipment 1 Heating or No-Load Sequence