This paper continues the series of the Fornax Deep Survey (FDS). Following the previous studies dedicated to extended Fornax cluster members, we present the catalogs of compact stellar systems in the Fornax cluster as well as extended background sources and point-like sources. We derive ugri photometry of ~1.7 million sources over the $sim$21 sq. degree area of FDS centered on NGC1399. For a wider area, of $sim$27 sq. degs extending in the direction of NGC1316, we provide gri data for ~3.1 million sources. To improve the morphological characterization of sources we generate multi-band image stacks by coadding the best seeing gri-band single exposures with a cut at FWHM<=0.9 arcsec. We use the multi-band stacks as detection frames. The identification of compact sources is obtained from a combination of photometric and morphometric selection criteria taking as reference the properties of sources with well-defined classification from the literature. We present a preliminary analysis of globular cluster (GC) distributions in the Fornax area. The study confirms and extends further previous results. We observe the inter-galactic population of GCs, a population of mainly blue GCs centered on NGC1399, extends over $sim$0.9Mpc, with an ellipticity $sim$0.65. Several sub-structures extend over $sim$0.5Mpc along various directions. Two of these structures do not cross any bright galaxy; one of them appears to be connected to NGC1404, a bright galaxy close to the cluster core and particularly poor of GCs. Using the gri catalogs we analyze the GC distribution over the extended FDS area, and do not find any obvious GC sub-structure bridging the two brightest cluster galaxies, NGC1316 and NGC1399. Although NGC1316 is twice brighter of NGC1399 in optical bands we estimate a factor of 3-4 richer GC population around NGC1399 compared to NGC1316, out to galactocentric distances of 40 arcmin
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