You really should not have any problem with eps in Indesign. so long as it was created properly, with appropriate transparency in the first place.
The problem with transparency usually comes in when somebody created an eps that contains raster elements that do not have proper transparency, like clipping. Unfortunately, unless you made the eps, it can be hard to tell what's in it. You can open the eps in AI, make a colored rectangle different than the colors in the eps and move the eps over the rectangle to check for transparency.
If you rasterize the eps you lose all the vector benefits, as long as the eps is pure vector in the first place.
Don't know exactly what you mean by a bounding box showing. Click on preview mode (bottom right on the tool pallette, and see if it disappears. Normal layout mode in ID shows all bounding boxes.
PDFs exported from ID at the proper quality (generally Press) will be fine - same as those from distiller. ID will also allow you to create and save custom pdf export settings for specific needs. Unless they've changed in the newer version, the one problem is pure grayscale pdfs. ID does not make them. If you need pure grayscale, with things like only grayscale color bars, for things like newpaper ads, it's best to print a grayscale postscript file and distill that.
Using OSX 10.3.9 on a G4 & G5