I don't think GoDaddy ever supported Moodle. GoDaddy is a hosting company, not a Moodle provider. Yes, of course they had one button scripts to install Moodle. I found it worked. But to upgrade Moodle, you were on your own. I don't think GoDaddy directly supports any application on their servers.
Having said this, I will mention that I have used GoDaddy for around 5 years, including their low end hosted account, and now one of their VPSs. I am not a big site, I run around 10-15 courses per year, maybe 200 students in total. I just upgraded from Moodle 2.3.+ to Moodle 2.4 earlier this week. Everything went fine.
I have a Moodle VPS with cPanel. I had trouble with Plesk, but it could have been my problem (lack of knowledge).
I know others have had problems with GoDaddy, but somehow, GoDaddy works for me.
(I don't own stock in GoDaddy, nor am I directly connected with this company in any way.)