Hi UCKAN,
Good questions!
1/ The flaps on many transport aircraft are big and complicated. They may have several panels, e.g. The wing, a slot, fore-flaps, a second slot, the main flap and even another slot followed by a third section.
The drive mechanism and support structure is designed to move the flaps in and out and to hold them in postiton for a short period of time at a reasonable manoeuvring speed. As with all things in aircraft design, there is a compromise between strength, weight and durability.
Sure, you could extend the flaps at the limit speed and use them to help decellerate the aircraft. This may be fine the first hundred times but on the 101st time you may start developing cracks, deformation or other damage in the flaps or in the drive and support mechanism. So, to avoid unnecessary maintenance costs, operators generally have an SOP that discourages use of flaps as speedbrakes and also encourages waiting until 15-20 knots below the limit speed before extending the next stage.
The FCOM for the 747-400 for example has a statement that says something like:
"Flight with flaps extended for prolonged periods, other than holding in the vicinity of an airfield, is prohibited. Flaps 10 or greater should not be used for prolonged holding or other extended periods of flight.
When holding with flap extended, limit speed to 250 K for flaps 1 and 230 K for flaps 5."
So, the best way to decellerate is to:
Think ahead (descend early, extra track miles, etc.);
Use speedbrakes;
Use the Gear;
All the time, extending flaps according to the recommended speed schedule.
2/ The balloon effect occurs when a particular flap extension produces a marked change in trim and/or lift coefficient. The effect may be to cause the flightpath to diverge upwards and therefore to require a lower nose attitude to maintain the desired trajectory.
How to deal with it? Again, being aware that it will happen is half the answer. Be ready to adopt the appropriate attitude as the flaps move. Keep in trim. If intercepting an ILS glideslope from just below, watch out for GS capture as the balloon takes effect. If intercepting from above, be aware that you will need to increase drag before extending the flaps to the 'balloon setting'.
If possible, explore all of this in the sim with some free-play time and get the hang of your aircraft!