Be very, very careful. The missing certificate can be issued again, if appropriate documents are supplied. However, this combined with a suspension of licences for the area is not a good sign.
Unfortunately, legal permissions for land to be classed as urbanizable (legal to build on and not agricultural etc) do not come from the central government but from local government. One mayor can reclassify land as urbanizable - sometimes because of enconomic interests, or quite simply because a brown envelope was passed over containing lots of euros!
The next mayor might then look at the planning and decide that this land should not have been built on and declare it illegal. You might think that this is then the problem of the local council - but it won´t be. The people who own the property will lose out, not the people who reclassified the land, sold the land, built the properties, sold the properties etc. only the poor owner will be left holding a worthless property which could even be demolished, or at best be worth nothing and impossible to resell.
The other point to bear in mind is that a suspension of licences can go on for a really long time. Next year comes and goes, then another year. Friends of mine are in a limbo state on an urbanisation because the licences were frozen in the late 70´s. Next year was always promised, now it´s 2010! They have been told that next year everything will definitely go ahead - but they have heard that so many times.
Another point to bear in mind is that the property market is in a slump in Spain. This will affect future building and licences being issued, as there is a huge stock of unsold property lying idle and half completed urbanisations with licences but unable to sell the plots and buildings.
There are lots of bargains to be found at the moment so look around carefully and don´t rush into anything that has any doubts!