The easiest way is to add comment to the entry … and then toggle disabled flag by searching the comment. E.g.
/ip firewall address-list
add address=192.168.88.88/32 list=somelist comment="My address #1"
# from some script set the address list entry disabled
/ip firewall address-list set [ find comment="My address #1" ] disabled=yes
# ditto to enable it
You can even enable or disable number of address list entries if they have same comment set. You can use other properties in [ find … ] construct, such as list name …