Fungus is found in guinea pigs. Mites and lice are also found. They both cause itching and can cause hair loss too. When we've had mites or lice there hair loss has been more usual at the back end. We also see little black bits deep in the fur - usually around the rump - which are the debris and poop from these critters. But mites themselves are too small to be seen. Also, my long-haired piggy gets bits of dirt buried in her fur from the hay so it's kind of hard to tell on these long-haired ones what is actually happening!
There are drops (in this country they contain an active ingredient called Ivermectin) that are spotted on to the skin to treat mites or lice. When we've had them the piggy gets the first dose, then 2 weeks later a second dose, then after that usually a 3rd dose again after 2 weeks. This is because the stuff kills live critters but not eggs so the eggs have to hatch out before they can be treated. Ideally an infestation is cleared after 2 doses but our vets usually say to do 3 just in case some escape and the problem returns a few months later. If you have been given mite drops and the problem is mites the itching should stop within a day or so and piggy will be fine until new eggs start hatching out - then itching will return by the time you are ready for the second dose 2 weeks later. If you do not have mites or lice the drops will not harm piggy - they just won't cure him and he will itch just the same. Maybe the vet called them 'allergy' drops because people can freak out a bit when mites or lice are mentioned but the ones piggies usually get don't go on to people. When my pigs have got them it's usually because I've introduced a new piggy who has brought them in and infested the others - and it sounds like you have had him for quite a while?
I had an old fluffy girl and she did develop a fungus problem with her skin. It was not the dreaded 'ringworm' fungus that can be passed to people - it was something less contagious because her cage-mates never got it. My vet said older piggies can be prone to fungus problems as their immune systems are not so good and the fungus can take hold. It does cause itching. The vet prescribed me a special guinea-pig anti-fungus shampoo - I'm sorry I can't remember the name because it was some years back but it was definitely vet-strength and not something we could just buy in a shop here. I don't shampoo my pigs normally - they are fine cleaning themselves - but I had to shampoo with this medicated stuff, rinse clean and then carefully dry with a towel - then I put her on warm dry towels in a warm part of the house until she was completely dried off. This was repeated 3 times (I think one week apart - might have been longer). The good news is that it worked and her skin and fur looked much better. The awful part is that on the final rinse of the last shampoo she snuffed a drop of water up her nose, sneezed and then a few hours later started to go downhill very fast. The poor old girl actually died from inhaling that bit of water - when I saw she was unwell I rushed her to the vet but they said it was too late. The drop had triggered something and her lungs were already filling with fluid so there was nothing they could do for her. I was heartbroken and blamed myself very much. I wish I had used a flannel or cotton pads to try and wipe any shampoo from her face so that drop would have not trickled down. So that is something to be very careful about if you are using any sort of shampoo - my girl was very good considering she didn't like the process but she tolerated it and did like being on the warm towels with hay to munch and little treats. Sometimes they panic and try to leap out of the sink which can make protecting their airways even trickier.
This is not exactly encouraging I know, but it helps to have more information sometimes. If the vet gives you fungal shampoo just take you time and mind those airways. I hope he can feel better soon x