ConnectApi.BotVersionActivation.updateVersionStatus() can be used to Activate or Deactivate Salesforce BOT Version using Apex.

Please check the following sample apex code for your reference.

Sample Apex Code:

Id BOTVersionId = '0X9Ho000000l3uFKAQ';

try {
    
    ConnectApi.BotVersionActivationInfo activationInfo =
        ConnectApi.BotVersionActivation.updateVersionStatus ( 
            BOTVersionId, ConnectApi.BotVersionActivationStatus.InActive, 
            null 
        );
    
    System.debug( 
        'Chatbot Version Activation Info' + 
        activationInfo.toString()
    );
    
} catch ( Exception e ) {
    
    System.debug( '--- General Exception ---' );
    System.debug( 'Message: ' + e.getMessage() );
    
}

Note:

You can use:

ConnectApi.BotVersionActivationStatus.Active – to activate

ConnectApi.BotVersionActivationStatus.InActive – to deactivate

Agentforce Agent and Einstein BOT can be activated or deactivated using this approach.

Salesforce Article:

https://developer.salesforce.com/docs/atlas.en-us.apexref.meta/apexref/apex_ConnectAPI_BotVersionActivation_static_methods.htm

You can use the following SOQL to query the BotVersion object/entity.

SELECT Id, DeveloperName, BotDefinition.MasterLabel, 
BotDefinition.DeveloperName, BotDefinition.Type
FROM BotVersion

Salesforce Article:

https://developer.salesforce.com/docs/atlas.en-us.object_reference.meta/object_reference/sforce_api_objects_botdefinition.htm