Hi,
Once you have migrate the menu configuration in the new system, the previous "associated modules" won't be required anymore.
So, in that specific case, yes, you would be able to delete them.
But I recommend to perform a backup before, if you need to restore a module that you delete by mistake (or which is still used).
Regards,
Jerome - Obsidev.com
HikaMarket & HikaSerial developer / HikaShop core dev team.
Also helping the HikaShop support team when having some time or couldn't sleep.
By the way, do not send me private message, use the "contact us" form instead.