https://blender.stackexchange.com/questions/56795/script-outdated-shape-keys-and-applying-subdivision-surface-modifier/209214#209214

SuperApplyModifiers.py

# https://blender.stackexchange.com/questions/56795/script-outdated-shape-keys-and-applying-subdivision-surface-modifier
import bpy

def reset_shape_keys ():    
    for name, shape_key in get_active_block().items():
        shape_key.value = 0

def get_active_block ():
    if bpy.context.object.active_shape_key is None or bpy.context.object.active_shape_key.id_data is None:
        bpy.context.object.active_shape_key_index = 0
    block_id = bpy.context.object.active_shape_key.id_data.name
    return bpy.data.shape_keys[block_id].key_blocks

def select (selection):
    bpy.ops.object.select_all(action='DESELECT')
    selection.select_set(True)
    bpy.context.view_layer.objects.active = selection

def select_last_shape_key ():
    shape_key_count = len(get_active_block().items())
    bpy.context.object.active_shape_key_index = shape_key_count - 1

def remove_shape_keys (object):
    selection = bpy.context.object
    object.shape_key_clear()
    select(selection)

def apply_modifiers (object):
    selection = bpy.context.object
    select(object)

    for key, modifier in object.modifiers.items():
        if key != 'Armature':
            bpy.ops.object.modifier_apply(modifier=key)

    select(selection)        

def super_apply_modifiers ():
    original = bpy.context.object
    bpy.ops.object.duplicate_move(OBJECT_OT_duplicate={
        "linked":False, "mode":'TRANSLATION'}, 
        TRANSFORM_OT_translate={
            "value":(0, 0, 0), 
            "constraint_axis":(False, False, False), 
            "orient_matrix":[[0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0]],
            "orient_matrix_type":'GLOBAL',
            "mirror":False, 
            "use_proportional_edit":False, 
            "proportional_edit_falloff":'SMOOTH', 
            "proportional_size":1, 
            "snap":False, "snap_target":'CLOSEST', 
            "snap_point":(0, 0, 0), 
            "snap_align":False, 
            "snap_normal":(0, 0, 0), 
            "gpencil_strokes":False, 
            "texture_space":False, 
            "remove_on_cancel":False, 
            "release_confirm":False, 
            "use_accurate":False
        })
    
    backup = bpy.context.object
    backup.name = original.name + '_backup'
    remove_shape_keys(original)
    apply_modifiers(original)

    try:
        for key, shape_key in get_active_block().items():
            select(backup)
            if(key == "Basis"):
                continue
            bpy.ops.object.duplicate_move(
                OBJECT_OT_duplicate={"linked":False, "mode":'TRANSLATION'}, 
                TRANSFORM_OT_translate={
                    "value":(0, 0, 0), 
                    "constraint_axis":(False, False, False), 
                    "orient_matrix":[[0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0]],
                    "orient_matrix_type":'GLOBAL',
                    "mirror":False, 
                    "use_proportional_edit":False, 
                    "proportional_edit_falloff":'SMOOTH', 
                    "proportional_size":1, 
                    "snap":False, 
                    "snap_target":'CLOSEST', 
                    "snap_point":(0, 0, 0), 
                    "snap_align":False, 
                    "snap_normal":(0, 0, 0), 
                    "gpencil_strokes":False, 
                    "texture_space":False, 
                    "remove_on_cancel":False, 
                    "release_confirm":False, 
                    "use_accurate":False
                })
            
            print("key: " + key);
            meshed_shape_key = bpy.context.object
            meshed_shape_key.name = backup.name + '_' + key
            select(meshed_shape_key)
            reset_shape_keys()
            get_active_block()[key].value = 1
            bpy.ops.object.convert(target='MESH')

            select(original)
            meshed_shape_key.select_set(True)
            bpy.ops.object.join_shapes()
            select_last_shape_key()
            bpy.context.object.active_shape_key.name = key
            select(meshed_shape_key)
            bpy.ops.object.delete(use_global=False)
        
        backup.hide_set(True)

    except Exception as err:
        original_name = original.name
        original.name = original.name + "_broken"
        backup.name = original_name
        select(original)
#        bpy.ops.object.delete(use_global=False)

super_apply_modifiers()