They can lie of course but if they do the FDA/EMA will know, clinical trails and pharmacovigilance is very rigorous, if side effect numbers differ from what the MAH says the regulatory agencies will change the SPC/PIL.
When it comes to long term effects of the drug the pharmacovigilance will pick up any signals the drug gives, in the EU for example side effects data is collected and reviewed every 5 years, meaning all data on the drug since it has been on the market is reviewed, any changes in ADR statistics are reviewed to see if the product is still safe and appropriate changes in the SPC/PIL are made.
In the US data is reviewed constantly not periodically so if this increase in ADR in long term use is true the FDA will report on it. The FDA is not bought by a company, they wont classify data like that, they have no incentive to do so.
Side effects feel more pronounced as those who have them complain about them, those who don't not always say so. For example I am on finasteride and dutasteride and have no sides, I never talk about that, and I'm sure most people also don't. Millions take finasteride, having people on a forum like this (which is a place to talk about sides, meaning it seems more pronounced) may make it seem like way more than 2% experience these sides, but in reality all you are seeing is a very small percentage of the patients on the drug.