The lack of MagSafe is the biggest downside of the 16e to me.
I get why they did it. Sure it saves a tiny bit of production cost, but they omitted it so enthusiastic people on more of a budget who waited for the 16e can be upsold to the regular 16 (or Pro) more easily. The actual target demographic (so people actually buying the 16e instead of getting upsold) mostly doesn't care about MagSafe anyway.
So no, it won't hurt the 16e sales in any meaningful way and will likely lead to more upsells.
The problem I have with the omission of MagSafe is that there's now even less incentive to invest into the MagSafe/Qi2 ecosystem because a device that'll likely see a lot of sales lacks support for it. Yes, you can add the magnetic functionality via a case, but it's not there by default and that is actually a big deal.
I don't upgrade to every single generation of a given device Apple releases, but I usually buy "Pro" tier devices that are mostly fairly specced out as well.
Part of the reason I buy these devices is the ecosystem with its various subsystems, MagSafe being one of them. This subsystem is weaker if Apple itself doesn't support it on all of their latest devices.
So all these omissions related to ecosystem "subsystems" like MagSafe, UWB and even dynamic island (less incentive for devs to add live activities if fewer users can take advantage of them) are somewhat annoying to me.