The same issue happens when you define a complete new tool with a shortcut using bl_keymap. On first Add-on activation, the shortcut works. On restarting Blender, it is non-functional. But if you reload all scripts while Blender is still running, the shortcut works again. I have used this class from the Templates to verify this behavior:

bl_info = {
    "name": "Shortcutter",
    "author": "Bug Reporter",
    "version": (1, 0),
    "blender": (2, 80, 0),
}

import bpy
from bpy.types import WorkSpaceTool

class MyTool(WorkSpaceTool):
    bl_space_type='VIEW_3D'
    bl_context_mode='OBJECT'

    # The prefix of the idname should be your add-on name.
    bl_idname = "my_template.my_circle_select"
    bl_label = "My Circle Select"
    bl_description = (
        "This is a tooltip\n"
        "with multiple lines"
    )
    bl_icon = "ops.generic.select_circle"
    bl_widget = None
    bl_keymap = (
        ("view3d.select_circle", {"type": 'LEFTMOUSE', "value": 'PRESS'},
         {"properties": [("wait_for_input", False)]}),
        ("view3d.select_circle", {"type": 'LEFTMOUSE', "value": 'PRESS', "ctrl": True},
         {"properties": [("mode", 'SUB'), ("wait_for_input", False)]}),
    )

    def draw_settings(context, layout, tool):
        props = tool.operator_properties("view3d.select_circle")
        layout.prop(props, "mode")
        layout.prop(props, "radius")


def register():
    bpy.utils.register_tool(MyTool, after={"builtin.scale_cage"}, separator=True, group=True)

def unregister():
    bpy.utils.unregister_tool(MyTool)

if __name__ == "__main__":
    register()

Is this something that's on the ToDo list for 2.81 already? Or is there a workaround for it? Not being able to have modifier keys for custom tools limits the use quite a bit.

when will solve this problem? I can't advance because of it in my development

Hi @Max Derksen (Derksen) , if you are looking for a workaound for the problem of custom tools not working on Blender restart, you will find it in addons/mesh_snap_utilities_line/__init__.py
A simplified version of it is in: https://raw.githubusercontent.com/Shriinivas/blenderbezierutils/master/blenderbezierutils.py
(Essentially, you would need to register the tool and keymap in some roundabout way)

@Shrinivas (Shrinivas) (Shrinivas) , thanks, I'll try this for the instrument. What about saving the shortcuts in the settings addon? that doesn't work either

@Max Derksen (Derksen) Maybe there is also an option for saving the shortcuts in the workaround. Just check keys.py in snap utilities.
I am an add-on developer and faced the same issue in my tool. I got the pointer about this workaround from one of the users (thanks @yoshiki nosaka (sakana3)).