There is no problem with installing junction boxes above a suspended ceiling, as long as the box is less than 100 in.³ and securely fastened. National Electrical Code has this to say...
National Electrical Code 2014
Chapter 3 Wiring Methods and Materials
Article 314 Outlet, Device, Pull, and Junction Boxes; Conduit Bodies; Fittings; and Handhole Enclosures
II. Installation
314.23 Supports. Enclosures within the scope of this article shall be supported in accordance with one or more of the provisions in 314.23(A) through (H).
(D) Suspended Ceilings. An enclosure mounted to structural or supporting elements of a suspended ceiling shall be not more than 1650 cm3 (100 in.3) in size and shall be securely fastened in place in accordance with either (D)(1) or (D)(2).
(1) Framing Members. An enclosure shall be fastened to the framing members by mechanical means such as bolts, screws, or rivets, or by the use of clips or other securing means identified for use with the type of ceiling framing member(s) and enclosure(s) employed. The framing members shall be adequately supported and securely fastened to each other and to the building structure.
(2) Support Wires. The installation shall comply with the provisions of 300.11(A). The enclosure shall be secured, using methods identified for the purpose, to ceiling support wire(s), including any additional support wire(s) installed for that purpose. Support wire(s) used for enclosure support shall be fastened at each end so as to be taut within the ceiling cavity.
Code Violations
In the first image, the wires being spliced together like that violates NEC 300.15.
300.15 Boxes, Conduit Bodies, or Fittings Where Required. ... Where the wiring method is conduit, tubing, Type AC cable, Type MC cable, Type MI cable, nonmetallic-sheathed cable, or other cables, a box or conduit body shall be installed at each conductor splice point, outlet point, switch point, junction point, termination point, or pull point...
I've also noted some violations in the second image.

Click for larger view
Buy a ceiling hugger style fan (the ones without a stem or with the option to mount without the stem).
Mount the fan's bracket directly to the ceiling with toggle bolts or other such fastener. This way the fan is not support by the box at all.
Good luck with your project!
Best Answer
Nope on "covering-up", but Yep to put the original or new covers on them.
Junction boxes & any other electrical boxes have to remain accessible & so do all plumbing valves. Home Improvement places have access doors, panels & covers for all sizes of holes you'll need to leave in the drywall.