With the upcoming release of POI 4.1.0 (expected around February 2019), Apache POI will now have the ability to embed fonts as well. The methods provided are just the beginning, as it's not a simple task of adding .ttf/.otf files.
To convert True-Type (.ttf) or Open-Type (.otf) fonts to EOT/MTX formats compatible with Office, I'm utilizing sfntly. Since sfntly classes aren't available as maven artifacts yet and importing the whole chunk into POI isn't ideal, you can clone and customize my example project from here.
If you need to add an MTX font stream to a slideshow (HSLF or XSLF), you would use:
org.apache.poi.sl.usermodel.SlideShow.addFont(InputStream fontData)
To subset fonts, you'll require the specific codepoints used, which can be extracted using:
org.apache.poi.sl.extractor.SlideShowExtractor.getCodepoints(String typeface, Boolean italic, Boolean bold)
For retrieving information about an MTX font data stream, there is a new helper class available:
org.apache.poi.common.usermodel.fonts.FontHeader