Hi Keith,
It will be much easier to help if you could answer the following barrage of questions, sorry there are quite a lot.
The first thing to ask is what are the exact numbers for both the ammonia and nitrite tests, and who did the tests, you or a shop, and using strips or liquid reagent tests?
When did you set the tank up (you said a few weeks, but how many or weeks or months ago) and did you do a fishless cycle using ammonia before you bought the first fish?
If you did not do a fishless cycle, did you monitor ammonia and nitrite in the water during the weeks since the fish went in the tank?
How did you add the fish, all at once or a few at a time? If a few at a time, which order did you get them?
What is the volume of your tank?
OK, the reasons behind all those questions.
If a shop tested your water, they are fond of words like fine and OK when the results are not fine or OK. Some testers also say things like the result is in the normal range. Anything other than zero for both ammonia and nitrite is not OK. And strips are not as accurate as liquid reagent testers. The first set of questions is to find out the actual level of ammonia and nitrite and whether the testers were more or less likely to be accurate.
I asked how long the tank had been set up to find out if you have just set it up or if it has been running a few weeks/months or even years. Newly set up tanks with fish in can suffer from 'new tank syndrome' and your answers will give an indication if this is the problem.
If you did a fishless cycle with ammonia before getting fish, the problem with the guppies is likely to have a different cause than if you just put water in the tank, let it run a couple of days then got fish.
Even if you did not do a fishless cycle, adding the fish a few at a time will cause less problems than adding them all at once. But unless the tank was fishless cycled, the first fish in the tank will be more prone to health problems. If you did not monitor ammonia and nitrite daily from when the first fish went in, the first ones could well have been subjected to high levels of ammonia and nitrite which if they don't kill the fish outright will cause problems later down the line.
Guppies are notoriously weak fish. They have been very inbred to get those colours and a lot of breeders use weak fish to breed from. They do commonly die quite soon after purchase. I gave up trying to keep guppies years ago. If they were among the first fish in the tank, they won't cope well with a fish-in cycle. And even if they were last or you did a fishless cycle, you could have bought from a bad batch of fish.
Shrimps are experts at hiding. And you have some fish they will want to hide from, mainly the mollies and bleeding heart and emperor tetras which will make a snack of any shrimps they find. And if your shrimps were red cherry shrimps, they are quite small and easily picked out. I'm afraid your shrimps are either hiding in fear of their lives or they are inside some of your fish.
And with shrimps, the other problem they have in a newly set up tank is that they are even more sensitive to ammonia and nitrite than fish are, so if the shrimps were put in the tank early on they could have died and then been eaten.
I asked how big your tank is because you have several shoaling fish in too small a number. You need a minimum of six of all five species of tetra. But the danger is that you don't have enough room for all those fish. You will probably need to choose one or two species, get more of them and rehome the others. Perhaps part-ex them for more of the species you want to keep if the shop will allow that.