I want to change my hotpost certificates by running this script:
ssh admin@SERVER_IP -p SSH_PORT "/file remove certif.key.pem"
ssh admin@SERVER_IP -p SSH_PORT "/file remove certif.crt.pem"
scp -P SSH_PORT certif.crt.pem admin@SERVER_IP:/
scp -P SSH_PORT certif.key.pem admin@SERVER_IP:/

My question:
Do I need to restart the MikroTIK or is it transparent(no restart needed)?

I tried it in a lab, here is the result.
You need to reimport the certificate and might have to reconfigure the service where the certificate should apply.
Import certificate:
/certificate import file-name=crt.pem passphrase="myPASS"
Apply certificate to HTTPS services:
/ip service set www-ssl address=0.0.0.0/0 certificate=crt.pem_0 disabled=no port=443

No need to reboot the mikrotik.