Yes, the floating hidden window always pops up on whatever workspace I am currently working on.

I thought about automatically hiding it, when switching to another workspace, but have not yet come around doing this.

I use a simple script to start emacs in case I accidentally close it:

  i3-msg 'exec emacs -name emacs-server' 
  i3-msg  \[instance=\"emacs-server\"\] move scratchpad;
  i3-msg  \[instance=\"emacs-server\"\] floating enable;
  sleep 1
  i3-msg  \[instance=\"emacs-server\"\] scratchpad show;
  i3-msg  \[instance=\"emacs-server\"\] move position 450px 0px;
  i3-msg  \[instance=\"emacs-server\"\] resize set 950 100 ppt
  i3-msg  \[instance=\"emacs-server\"\] scratchpad show;

The i3 config portion additionally has the key binding:

  bindsym $mod+less [instance="emacs-server"] scratchpad show