I believe you are talking about versions 2.9.x
ip webproxy is squid.
ip proxy is the new proxy entirely created by MikroTik.
I believe so much in Squid cause i use it in different Linux boxes, but in MikroTik it is a little bit unstable (ie, cache gets full and blocks the router, false error messages, etc)
Ip proxy instead, is doing great improvements with each release. With the latest release it seem very stable.
--Do you remember that guy who gave up? Neither does anybody else!