Ipe supports a simple model of transparency. You can set the opacity of path objects and text objects: an opacity of 1.0 means a fully opaque object, while 0.5 would mean that the object is half-transparent. All opacity values you wish to use in a document must be defined in its stylesheet.
Documents containing transparency cannot be saved in EPS format. (Postscript does not support transparency.) For this reason, the standard Ipe stylesheet (that is automatically added to newly created documents) does not define opacity values, and so you must use a custom stylesheet to make use of transparency in your document.